I've noticed a serious problem when I do W C to save merge results. If the destination file already exists I get prompted to overwrite. After typing Y to that prompt I find that ediff has saved it's own help buffer and not the `C' buffer. That is, the destination file contains only:
? -quick help
If the target doesn't exist already then it is created with the proper contents.
In my case all 3 files (the 2 being merged and the result file) are remote and have the same name in different directories. I don't believe these are requirements to recreate the problem. I did one test using local files where the destination filename was different from the sources and the problem still occurred. It appears it should be very easy to consistently recreate.
While I've got your ear; there doesn't seem to be a way to merge files residing on a remote system. I can only merge files accessible via the windows dialog box. I'm getting around this by visiting the files first then using ediff-merge-buffers. This method is quite tedious when merging changes to many files.
In GNU Emacs 22.0.50 (i386-msvc-nt5.0.2195)
of 2005-05-23 on LD1
Distributor `Microsoft Corp.', version 5.0.2195
configured using `configure --with-msvc (12.00)'
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value of $LANG: ENU
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