Put your source path back to what it was before and then add a path substitution to point your library to the new location. I don’t know why it would be crashing doing a clean library but you were going around this issue the wrong way. The other option would be to put your sources back to exactly the way they were before and then do a “change content” and set your source to none and select the option to clean your library when it asks there. Once your library has been cleaned of all the items with the old file paths only then should you change a file path and set content to allow scraping.
If you had already scraped the updated source and have a library full of duplicates then before changing to the old paths set content as none to remove the new items. That should (hopefully) then get you back to what you were before the duplicates, and then you can follow the aforementioned path.
Or you could just delete your library manually and start over from scratch if that is preferable
How to return Kodi to default settings
Let’s test with Kodi default settings. Enter the following commands with an SSH connection.
systemctl stop mediacenter
mv ~/.kodi ~/kodi.bak
systemctl start mediacenter
If needed you can restore:
systemctl stop mediacenter
mv ~/.kodi ~/kodi.bk2
mv ~/kodi.bak ~/.kodi
systemctl start mediacenter
If your original setup was restored as expected and you want get rid of the unneeded clean install you can delete that with the following command.
rm -r ~/kodi.bk2