I'm still using an older version, but is it possible to disable the restore to original button? I've pressed it by mistakes a few time and it is not really the kind of thing that you would use all of the time anyway.
I think it would be better to have the "restore.." in the tools menu rather than the main one. Wheras the other stuff you use continually while modding the Restore would only be used once before creating the mod.

That said, don't get me wrong, FLE is a great program and has made it possible to create much more than I would be able to otherwise.