I accidentially applied APEv2 tag to my FLAC files using tag.exe

How can I remove only the APEv2 tag? It seems that tag.exe has no option for that, and neigher foobar2000 or mp3tag can see this tag.

Ugly-hack solution: transcode to FLAC.

Seems not really to be a great solution for my 500GB FLAC collection

Actually I think I have an idea that should work the best (at least the quickest): Load the files into foobar2000 library, then use tag.exe recursively to remove all the tags. Then selecting all files in foobar2000 and use "Rewrite file tags".

mp3tag will remove them. If you've got enough info in your filenames you can then make mp3tag do filename->tag to get the info back

mp3tag: perform a "tag cut" and then a "tag paste".
The paste will only be in a FLAC tag and no info will be lost.

Are you sure it works on FLAC files? It can't see that theres an APE tag present. Also, does it work in batch?

I have done it (not in batch) on FLAC files with ID3 tags and it worked.
Do an experiment and you will know.

Worked like a charm. Though you should be very careful with this!