Can you perhaps put in a warning prompt if one hits Ctrl-Z, before performing the actual undo? I think this would prevent a lot of frustration from unintentional undo's.
I run into this situation a lot. I have modified a file or bunch of files at once (in one operation), then moved on to another file. I make a typo while typing in one of the tag fields and hit Ctrl-Z to undo it, expecting it to just undo my typing, a standard text box feature (like the text box I am writing this post in right now). Instead, it silently undoes all the changes I made to the previously modified file(s), not the selected one I am looking at, at worst leaving me unaware of what happened, at best making me wish there was a 'Redo' function. These accidental changes may be hard to repair from memory, especially if I do not realize what has happened until some time later, or worse, repeat the mistake multiple times.
I guess an alternate suggestion would be to make it possible to disable or remap Undo to another key.
Just a suggestion, and thanks for a great program.