I had that same issue, some .dat files were damaged when editing. That is why I recommend to do the following (Hope the instr is not too long!)
1. Always keep a backup copy of the original battle.fs/fl files in a separate location!!!
2. When you find out that one of the .dat file is damaged, go to the dir where you have extracted them
3. Delete damaged files
4. Use Ifrit's tools to extract ONLY the removed .dat files from the original back-up battle.fl (select one at a time, in the case before my message, 19.dat 47.dat and 76.dat)
5. Try again, do NOT give up
6. Now you should be able to edit again without bizarre effects
7. All other edited .dat files have NOT lost user made modifications, so you "lose" only the damaged files.
+ I found this out when my game crashed when it tried to load Creeps' data, found out the file was damaged (it tried to load Elastoid's data o.o ) Did the delete-extract-replace and now, everything OK!
And to the other message about magic list, I found out the following
Select "MAGIC" from the list, ability # of your choice and Animation should be #11
Use the draw list in the tool! The abilities are in order, example 1. ability is Fire, 11. Aero, 23. Curaga and so on. Make a txt file with the list in order, and number every skill. That way you can modify the magic spells enemies use.
31 11 = Reflect
16 11 = Meteor
Same goes for the items, however I am not 100% sure about Anim number in Items.
I hope this helps, I am very new to this forum, and so far I have only modded FF9.
English is not my native, greetings from frozen Finland <3