bug#40838: 28.0.50; [feature/native-comp] Function overrides in init.el are not honored after deferred compilation

[Ihor Radchenko]

I redefine or patch some functions from packages in my init.el.
However, I noticed that the default definitions can be unexpectedly
restored.

I observe the following when comp-deferred-compilation is set to 't:

1. A package that is not native-compiled is loaded on startup and the
native-comp process is started asynchronously
2. Some function from the package is redefined in my init.el 
3. The native compilation finishes
4. My function definition from init.el is no longer working. The default
version is restored.

I do not think that loading .eln files should override function slots if
they are different from what is in the original .el file.

Best,
Ihor

In GNU Emacs 28.0.50 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.16, cairo 
version 1.16.0)
 of 2020-04-24 built on yantar92-laptop
Repository revision: 81389d5f2dcb41730dcbc76874cc14eadb53ae75
Repository branch: feature/native-comp
Windowing system distributor 'The X.Org Foundation', version 11.0.12006000
System Description: Gentoo/Linux

Configured using:
 'configure --with-nativecomp'

Configured features:
XPM JPEG TIFF GIF PNG RSVG CAIRO SOUND GPM DBUS GSETTINGS GLIB NOTIFY
INOTIFY ACL GNUTLS LIBXML2 FREETYPE HARFBUZZ ZLIB TOOLKIT_SCROLL_BARS
GTK3 X11 XDBE XIM MODULES THREADS PDUMPER LCMS2 GMP

Important settings:
  value of $LANG: en_US.utf8
  value of $XMODIFIERS: @im=imsettings
  locale-coding-system: utf-8-unix

Major mode: Lisp Interaction

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Features:
(shadow mail-extr emacsbug sendmail avy mule-util misearch multi-isearch
texmathp conf-mode helm-x-files tramp tramp-loaddefs trampver
tramp-integration files-x tramp-compat ls-lisp cal-iso sh-script
executable gnuplot-gui gnuplot hideshow flycheck-tip error-tip
flycheck-tip-autoloads flycheck rainbow-delimiters highlight-numbers
parent-mode easy-escape org-duration vc-git sort
yasnippet-snippets-autoloads yasnippet-snippets yasnippet ffap
org-table-sticky-header ol-eww ol-rmail ol-mhe ol-irc ol-info ol-gnus
nnir ol-docview doc-view ol-bbdb ol-w3m dired-hide-dotfiles ol-notmuch
org-eldoc doom-themes-ext-org doom-themes doom-themes-base
doom-themes-autoloads org-table-sticky-header-autoloads pretty-symbols
posframe posframe-autoloads ob-async ob-async-autoloads ob-latex ob-dot
ob-calc calc-store calc-trail calc-ext calc calc-loaddefs calc-macs
ob-gnuplot ob-ditaa ob-C cc-mode cc-fonts cc-guess cc-menus cc-cmds
cc-styles cc-align cc-engine cc-vars cc-defs ob-python ob-perl ob-org
ob-shell org-tempo tempo ox-md ox-extra doct doct-autoloads
org-capture-pop-frame org-capture-pop-frame-autoloads org-protocol
pomidor-autoloads org-clock org-autosort helm-org-contacts
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gnus-group gnus-undo gnus-start gnus-cloud nnimap nnmail mail-source
utf7 netrc nnoo gnus-spec gnus-int gnus-range gnus-win helm-org-ql
helm-org helm-org-autoloads org-ql-search org-ql-view ov org-ql peg
org-super-agenda ts org-ql-autoloads peg-autoloads ov-autoloads
org-super-agenda-autoloads ts-autoloads map-autoloads
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nxml-enc xmltok nxml-util ox-latex ox-icalendar ox-html table ox-ascii
ox-publish ox org-ref-glossary org-ref-bibtex org-ref-citeproc
org-element key-chord doi-utils org-ref-utils org-ref-pdf ol-bibtex
bibtex htmlize org-ref-autoloads key-chord-autoloads ivy-autoloads
helm-bibtex-autoloads bibtex-completion-autoloads biblio-autoloads
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notmuch-maildir-fcc notmuch-address notmuch-company notmuch-parser
notmuch-wash coolj notmuch-query goto-addr icalendar diary-lib
diary-loaddefs notmuch-tag notmuch-lib notmuch-compat mm-view mml-smime
smime dig notmuch-autoloads elfeed-score elfeed-org elfeed-org-autoloads
org-autoloads quick-peek quick-peek-autoloads elfeed-show elfeed-search
shr svg dom elfeed-csv elfeed elfeed-curl elfeed-log elfeed-db
elfeed-lib avl-tree url-queue xml-query elfeed-score-autoloads
elfeed-autoloads mingus libmpdee mingus-autoloads libmpdee-autoloads
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semantic/wisent/comp semantic/wisent semantic/wisent/wisent
semantic/util-modes semantic/util semantic semantic/tag semantic/lex
semantic/fw mode-local cedet pdf-misc pdf-view magit-bookmark bookmark
pp jka-compr pdf-cache pdf-info tq pdf-util pdf-tools-autoloads
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tex-ispell tex-style tex dbus xml auctex-autoloads tex-site lua-mode
lua-mode-autoloads gnuplot-autoloads el-patch el-patch-autoloads eros
rsw-elisp warnings eros-autoloads ht ht-autoloads nameless lisp-mnt
nameless-autoloads paredit paredit-autoloads bug-hunter
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ob-emacs-lisp ob-core ob-eval org-table ol org-keys org-compat org-macs
org-loaddefs cal-menu calendar cal-loaddefs disk-usage
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all-the-icons-dired-autoloads dired-async dired-open-autoloads
dired-hacks-utils dired-hacks-utils-autoloads dired+ image-dired
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dired-aux dired+-autoloads winner windower emacs-windower-autoloads
recentf tree-widget helm-command helm-elisp helm-eval edebug backtrace
helm-info helm-mode helm-files helm-buffers helm-occur helm-tags
helm-locate helm-grep helm-regexp helm-utils helm-help helm-types
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goto-line-preview goto-line-preview-autoloads avy-autoloads eval-sexp-fu
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rainbow-delimiters-autoloads highlight-parentheses
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epl-autoloads flyspell ispell hi-lock forge-list forge-commands
forge-semi forge-bitbucket buck forge-gogs gogs forge-gitea gtea
forge-gitlab glab forge-github ghub-graphql treepy gsexp ghub let-alist
gnutls forge-notify forge-revnote forge-pullreq forge-issue forge-topic
parse-time iso8601 bug-reference forge-post markdown-mode noutline
outline forge-repo forge forge-core forge-db closql emacsql-sqlite
emacsql emacsql-compiler url-http url-auth url-gw nsm url url-proxy
url-privacy url-expand url-methods url-history url-cookie url-domsuf
url-util mailcap forge-autoloads closql-autoloads
emacsql-sqlite-autoloads emacsql-autoloads magithub-autoloads
markdown-mode-autoloads ghub+-autoloads apiwrap-autoloads ghub-autoloads
treepy-autoloads let-alist-autoloads magit-submodule magit-obsolete
magit-blame magit-stash magit-reflog magit-bisect magit-push magit-pull
magit-fetch magit-clone magit-remote magit-commit magit-sequence
magit-notes magit-worktree magit-tag magit-merge magit-branch
magit-reset magit-files magit-refs magit-status magit package browse-url
url-handlers url-parse auth-source json map url-vars magit-repos
magit-apply magit-wip magit-log which-func imenu magit-diff smerge-mode
diff diff-mode magit-core magit-autorevert magit-margin magit-transient
magit-process magit-mode git-commit magit-git magit-section magit-utils
crm log-edit message rmc puny dired dired-loaddefs rfc822 mailabbrev
gmm-utils mailheader pcvs-util add-log with-editor async-bytecomp async
shell pcomplete comint ansi-color transient format-spec magit-autoloads
git-commit-autoloads with-editor-autoloads transient-autoloads
autorevert filenotify disp-table company-oddmuse company-keywords
company-etags etags fileloop generator xref project company-gtags
company-dabbrev-code company-dabbrev company-files company-capf
company-cmake company-xcode company-clang company-semantic company-eclim
company-template company-bbdb company persistent-scratch
persistent-scratch-autoloads savehist backup-walker-autoloads
company-autoloads helm-autoloads helm-core-autoloads pyim-basedict pyim
pyim-probe xr pyim-common pyim-pymap popup pyim-autoloads
pyim-basedict-autoloads xr-autoloads async-autoloads popup-autoloads
avoid reverse-im quail reverse-im-autoloads boon-qwerty boon-powerline
centered-window centered-window-mode face-remap boon boon-moves
find-func er-basic-expansions expand-region-core expand-region-custom
boon-search boon-keys boon-main boon-arguments multiple-cursors
mc-hide-unmatched-lines-mode mc-separate-operations
rectangular-region-mode mc-mark-pop mc-mark-more thingatpt
mc-cycle-cursors mc-edit-lines multiple-cursors-core rect boon-regs
boon-utils boon-core boon-autoloads multiple-cursors-autoloads
expand-region-autoloads meta-functions hl-line footnote mml mml-sec
password-cache epa derived epg epg-config gnus-util rmail rmail-loaddefs
mail-utils text-property-search time-date mm-decode mm-bodies mm-encode
mail-parse rfc2231 rfc2047 rfc2045 ietf-drums mm-util mail-prsvr
spaceline-all-the-icons spaceline-all-the-icons-separators
spaceline-all-the-icons-segments all-the-icons all-the-icons-faces
data-material data-weathericons data-octicons data-fileicons
data-faicons data-alltheicons memoize spaceline-all-the-icons-autoloads
all-the-icons-autoloads memoize-autoloads spaceline-config
spaceline-segments s spaceline dash spaceline-autoloads s-autoloads
dash-autoloads smart-mode-line rich-minority smart-mode-line-autoloads
rich-minority-autoloads powerline advice powerline-separators color
powerline-themes powerline-autoloads latex-pretty-symbols
latex-pretty-symbols-autoloads pretty-symbols-autoloads page-break-lines
page-break-lines-autoloads font-utils unicode-fonts persistent-soft
list-utils pcache eieio-compat eieio-base eieio eieio-core
eieio-loaddefs unicode-fonts-autoloads ucs-utils-autoloads
font-utils-autoloads persistent-soft-autoloads list-utils-autoloads cl
pcache-autoloads centered-window-mode-autoloads shackle trace cus-edit
cus-start cus-load wid-edit shackle-autoloads use-package-diminish
flatui-theme flatui-theme-autoloads gcmh-autoloads pcase asoc
asoc.el-autoloads edmacro kmacro hydra ring lv hydra-autoloads
lv-autoloads finder-inf use-package-bind-key org-plus-contrib-autoloads
org-version bind-key easy-mmode diminish diminish-autoloads
use-package-core use-package-autoloads bind-key-autoloads
straight-autoloads info straight comp rx cl-seq cl-extra help-mode
easymenu seq byte-opt subr-x cl-macs gv cl-loaddefs cl-lib bytecomp
byte-compile cconv server tooltip eldoc electric uniquify ediff-hook
vc-hooks lisp-float-type mwheel term/x-win x-win term/common-win x-dnd
tool-bar dnd fontset image regexp-opt fringe tabulated-list replace
newcomment text-mode elisp-mode lisp-mode prog-mode register page
tab-bar menu-bar rfn-eshadow isearch timer select scroll-bar mouse
jit-lock font-lock syntax facemenu font-core term/tty-colors frame
minibuffer cl-generic cham georgian utf-8-lang misc-lang vietnamese
tibetan thai tai-viet lao korean japanese eucjp-ms cp51932 hebrew greek
romanian slovak czech european ethiopic indian cyrillic chinese
composite charscript charprop case-table epa-hook jka-cmpr-hook help
simple abbrev obarray cl-preloaded nadvice loaddefs button faces
cus-face macroexp files text-properties overlay sha1 md5 base64 format
env code-pages mule custom widget hashtable-print-readable backquote
threads dbusbind inotify lcms2 dynamic-setting system-font-setting
font-render-setting cairo move-toolbar gtk x-toolkit x multi-tty
make-network-process emacs)

Memory information:
((conses 16 1654234 2114834)
 (symbols 48 76184 918)
 (strings 32 308144 223444)
 (string-bytes 1 14335673)
 (vectors 16 164944)
 (vector-slots 8 2885629 1597084)
 (floats 8 6574 4670)
 (intervals 56 67210 17503)
 (buffers 992 58))

-- 
Ihor Radchenko,
PhD,
Center for Advancing Materials Performance from the Nanoscale (CAMP-nano)
State Key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong 
University, Xi'an, China
Email: yantar92@gmail.com, ihor_radchenko@alumni.sutd.edu.sg