Best way to merge two databases with large overlaps?

I’ve checked the Zotero library - there are 3816 entries. I then export to bib format

When I File>Open the bib file in Zotero the new library reports 3790 entries in JabRef

I also tried File> Import and the Import dialogue reported 3790 entries in the bib file. After Select All and Import, JabRef becme unresponsive and after 15 minutes I cancelled the process.

Import took longer than expected, but I assume it was running a lot of checks and I assume there is a log of issues reported? Wasn’t clear where to look

EDIT: I left it running and the successful import took 25 minutes, and reported 3790 entries too
The cleaned JabRef database has 3488 entries