Hey there link,
I just wanted to post and say that I'm looking at it some more now, after not even opening the source for a few months.. Now that I'm looking at it again, I'm not so sure the solution is as obvious as I thought it was.
If you use the MAMEWAH Config-sanctioned '_Installed Layouts' as your layouts folder, MC should work perfectly with keeping track of your layouts->emulator mapping no matter what you do with your emulator (delete, add, re-arrange). The issue creeps in when you don't use '_Installed Layouts' for your layout folder, and this is mostly on purpose.
I don't want MC to be destructive, or at least, I want it to be as least destructive as possible. That's why I went through the trouble of making a _backup folder whenever it changes a file and also the reason '_Installed Layouts' exists at all!
When you set your layouts folder to _Installed Layouts and save (File->Save), MC will rename everything in _Installed Layouts and add a "._mc" extension to avoid the chance of overwriting something. It will then look at all your emulators and the layouts you have defined for them and COPY them from other layouts folders into '_Installed Layouts' and leave your other layouts folders just as they are. Then, once all your layouts have been set up to match the emulator, MC will clean up after itself delete everything in '_Installed Layouts' with a ._mc extention (which by this time shouldn't be needed any more).
Now, I'm not sure I articulated the process as well enough, but my question is this: Things will be a little easier if I could take some liberties with other layout folders other than '_Installed Layouts', but I/we/you run the risk of potentially deleting data without recoverability options. Should I keep it the way it is with MC only managing your layouts if you have your layout folder set to '_Installed Layouts'?
The SAFEST way for this to work is to *require* that everyone who uses MC to set their layouts folder to '_Installed Layouts' (in which case I don't need to do anything to other layouts folders and the above scenerio doesn't apply), otherwise none of your layouts will match your emulators. That's probably not too big of a deal though, since it's not like MC will delete your other layouts folders and you could always go back once you stopped using MC. What do you think?
(Incidentally, I found the "bug" where some people were getting a folder full of files with ._mc extentions: When I was setting this whole process up I kind of stopped in the middle when it came time to make that decision above and never made a final decision... So MC renames everything in your layouts folder no matter what it is with a ._mc extention, and then doesn't necessarily put everything back if your layouts folder is not '_Installed Layouts'. I'll fix this once I have a decision.)
-sab
P.S. I know this doesn't address your issue with deleting an emulator, but once I straighten this out I'll be able to get a handle on the whole process and possibly re-write it. In any case, it will be easier to fix any problems.