Syncing two libraries (to merge) fails and deletes data

I'm trying to merge two libraries by syncing them. But after I synced the first library, and switched to the second library (same Firefox - I just changed the Custom Directory Location in the Zotero prefs)and then try to sync the second library, I got an error message (Uploaded data not well-formed (Report ID: 56b85f3aa3)), and many of the items had vanished from the second library (some collections were completely empty). Instead of doing the sensible thing and reporting the error, I recovered the second library from a back-up, and did it again (this time turning off File Syncing). This time there were no error messages, but the same failure to sync, and vanishing items.

When I check online, the collections from the second library are in my Library, but no items.

I checked the integrity of the database, and it reports as fine. But when I tried an alternative method and exported the second library as an RDF (with files and notes), I got an "Unresponsive script - Zotero RDF.js:330" warning, and it took about 5 minutes before Firefox resumed (for a library with 366 items and nothing in the trash). Attempting to import the resultant RDF file resulted in another error: "An error occurred while trying to import the selected file. Please ensure that the file is valid and try again."

Any ideas?
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