Quote - Can I still use the Custom categories feature in DS 4.6 Pro?

Yes.  Use the "Content DB Maintenance > Export User Data" function to back-up your custom categories.  It can take a long time if you have a lot of data -- I categorize everything my own way, and it can take 30-45 minutes to export, and I've heard from someone who has several hundred GB's of content that it takes over an hour for him.

Aside from giving you a back-up, this saves only the relative file locations.  So you can then reset your content database, split up your runtimes (making sure you add each new location to DS's list), and Re-Import Metadata (you can choose to import just the User Data if you don't want DAZ' default metadata also), and while importing the user data it will figure out which of the multiple runtimes each item is in.