Sample that happened:
I had two files, the one from [triad] and the one from [a.f.k]. I remove the one by afk with the red remove button in the mylist then the whole anime disappears from the mylist. Checked the anime manually and there the file by [triad] is still marked.
Second sample, ok so I have duplicate files for Ultra Maniac TV (710) too so I check the boxes with the files that I've removed and select the remove action and click the button. This anime disappears too! I guess it'll sync back later but it seems that if you remove 1 file for every episode you have then the anime disappears from your mylist!!
Guess it'll be back in two hours but it's still very confusing...
I can't reproduce this anymore and I could several times before, maybe you changed something. =)
I noticed mylist was updated immediatelly by !addfile, maybe that's what's different?