With no details of your books sources, how many books you loaded onto your Kobo, and are books loaded onto internal memory or SD card.
If your using SD card first format the card with full overwrite format option using the SD card Association formatting tool.
https://www.sdcard.org/downloads/for.../eula_windows/
If you just loaded 5000 books it will take a long time the reader to process those books. Then the question is it really still processing or hung up in some loop just spinning the processing indicator? We can only wish it would skip the problem books that can not be entered into database and list problem books. This bug has been around for years with no fix. Load a few books at a time makes it easier to find books causing your problem. If your loading 5000 books 1000 books might be a few books, but much fewer makes it easier to find problem book. So this might be inconvenient way to waste time. If your knowledgeable about database used by the reader you can look for the last book entered into data base which is one causing processing problem. Otherwise first load fewest books that must be on the reader then slowly add more until problem book is found.