USB > desktop > prime 4 workflow

So I have engine prime on my desktop, and use it there to analyse my collection, that creates an engine prime folder in my collection.

I use my prime 4 as an all in one, with USB, I dont use it as a controller.

So I have an engine prime folder on my desktop, and I copy that same folder to my USB, (I messed it up before and ended up with a broke cokkection), I use my prime 4, some songs the cues arent right or i set hot cues or loops. Then I update my collection on my desktop, and move the updated files and engine prime folder to my USB. Doing this removes all of my hotcues or cue points or loops because they are saved to the engine prime folder in the USB, not the desktop…

If I overwrite the engine prime folder on my desktop with the one from my USB before I open engine prime software… will this corrupt my db? I want to keep the database with the loops and move that around. In my head I should just be able to overwrite desktop folder, open engine, analyzed a few songs, copy all that back on to the USB and it be sweet…