Have you checked the recycle bin for the deleted modules? That would be my first worry - all my lost modules. If you can recover them, can you back them up to a different folder or sd card or thumb drive?
Being very careful so you don't lose files that you want... Have you tried creating a new folder and pointing SS to the new folder as your default for the user modules? Have you tried putting non-SwordSearcher files (just copies of other files, like jpg or txt files, for sure!) into the Documents/SwordSearcher User Modules folder and see if they disappear? Have you tried creating a module and before you exit SS, copy it to a different folder, exit SS, see if the module has been deleted, if it has, copy it back into the Documents/SwordSearcher User Modules folder and then open SS and see if the module is there? (That would check to see if the files are being deleted on exit or open.)
Have you reinstalled SwordSearcher? Are you losing any other files from other programs? Have you looked in the Task Manager for unknown programs that are running? Have you tried booting your computer in Safe Mode?
I can't think of anything else off the top of my head. I sure hope you get it figured out!