1. If I do some ASM hacking, and then apply a fftpatch to the ISO, will it erase my hacks?
2. (Related) Will applying a fftpatch to an already patched ISO cause any problems?
The answer to 2 is yes it will cause lots of problems.
The answer to number one is, its possible.
If you edit BATTLE.BIN, then apply a patch that has BATTLE.BIN edits in it, then yes, your edits will disappear. It all depends on what the patch is going to change.
If you're talking about doing some edits you find on this site, and then patching with FFTPatcher, then you probably won't have any problems. If you're talking about doing some edits you found on this site, and then applying a PPF patch, then you're edits will probably disappear.
If nothing else, do your edits after applying a PPF patch.