I did some tests with the Mp3Tag program for somebody. In the middle of that i remembered this thread, and included files treated with Mp3Gain. So here are the results:
Mp3Tag recognizes ApeV2 tags, but can't show them. However, it is able to delete such tags! I did so, and verified the resultat with a hex editor.
After that i played all three versions of my test file:
1. mp3 (pure)
2. mp3 (Mp3Gain with ApeV2 tags)
3. mp3 (Mp3Gain without ApeV2 tags)
Conclusion:
You don't loose the volume settings if ApeV2 tags are removed! (Of course, the backup data are lost, so you can't undo Mp3Gain's modifications.)
Mp3Gain obviously stores volume informations "within", not (only) as tags at the end of a file. This is not an unexpected result for me, however, because my very legacy standard mp3-player (Winplay3 from FhG) never had problems to correctly reproduce Mp3Gain treated files.
P.S.
My tests were restricted to Mp3Tag v2.39 because of system requirements. The newest version (2.42) has extended functions concerning some audio formats. The prog is freeware.
Link:
http://www.mp3tag.de (german/english)