URLs of item links in duplicated databases

If they retained the URL, wouldn’t they still be unique?

If you use File > Export > Files and Folders, the items will get new UUIDs when you import them.
If you drag and drop or use right-click > Move > …, the UUIDs should be preserved.

That being said, I do not advocate huge moves via these methods. Give your machine a break and do it in smaller chunks, instead of trying to do one massive move.