I lately have been only exporting folders with my module contents inside. I ran into this problem awhile back and had thought i already posted this problem.
When you add more than one exported module to your main library- when you load the library afresh after opening Developer one of those modules has it's folder(s) emptied and scattered into the different main default folders. The other added module in the library retains its contents in its folder. I think if you swap the order around in library its the second one that has its contents moved?
Folders are great for organization but this problem is annoying because if you have to modify a module for it to work in your new project its a lot of looking for the contents if the new project is fairly big.
The solution is to only have one module added to your library and manually add the other modules you want for a new project as those tasks and contents stay inside said module folder *when you import them manually*.
I do not know if this is local to exported module folders only.
I have sent you an email with the two modules (attached) that cause this bug, doesn't seem to happen with my other modules just these two, which if imported manually there is no conflict or error messages.