So does it notify Aspell of replacements one makes?
From what I think is most recent ispell.el from fsf emacs cvs,
$ grep -n ispell-send-replacement ispell.el
1440:(defun ispell-send-replacement (misspelled replacement)
3073: (ispell-send-replacement (car poss) replace)
3078: (ispell-send-replacement (car poss) replace-word)
with
(defun ispell-send-replacement (misspelled replacement)
"Notify aspell that MISSPELLED should be spelled REPLACEMENT.
This allows it to improve the suggestion list based on actual mispellings."
(and ispell-really-aspell
(ispell-send-string (concat "$$ra " misspelled "," replacement
"\n"))))
ispell.el is unmaintained upstream (as well s flyspell.el) and the most
actively modified one is that from fsf emacs cvs.