merged code from branch to MAIN

[Rick Oosterholt]

branch visualisation:

    /----- branch B -------
   /
--/-------- MAIN trunk ----

Our MAIN branch was very old, only development on branch B was
performed.
We wanted code from branch B to overwrite code in MAIN.
This was causing very many merge conflicts. So we copied files from a
branch B checkout to a MAIN checkout and commited the code.

Now, each time when we try to merge code from branch B to the MAIN
trunk, *ALL* files are flagged to be modified and many files give
merge conflicts.

How do we solve this problem? How can be do a branch merge again and
only modified files get merged?

Thanks in advance,
Rick Oosterholt