Spyder - UMD has deleted: module
Short Answer:
Perhaps deleted is not the best word in the message you mention. It should be reloaded, which is what UMD is really doing and because is way less confusing. I'll fill an issue for this in our issue tracker.
Long answer:
UMD reloads not only your script but also all the local modules it depends on. By local I mean modules outside your Python installation and over which you have writing permissions.
The idea is that next to your script, perhaps you have developed a library of auxiliary functions to go with it. So you most probably want to reload that library too, so that any changes to it are reflected at run time.
I know this is not your case, so if you want to remove that message, you can go to:
Tools > Preferences > Console > Advanced settings > User Module Deleter
and deactivate the option
Show reloaded modules list