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I merged my main catalog, which automatically writes xmp on file, with a catalogue that contained many duplicates but with no metadata on them, essentially creating a conflict. Lightroom dealt with the conflict by creating virtual copies of the duplicate files and moving all metadata on them, leaving the masters bare in the catalog and the directory. So now I have all my ratings, labels, keywords and collection information of 8,000 images on the virtual copies, not on the masters....
Rather than try to fix the result of the merge you've already done, it might be worthwhile to step back and reconsider how you did the merge. (That's assuming you have a backup of the two catalogs you can revert to, right?)
To test my understanding, you have two catalogs, call them A and B. B has many duplicate pics from A, and these duplicates have no metadata and are not placed in collections as they are in A. While in A, you imported from B, selecting the option Replace: Metadata And Develop Settings. Pics that were in B but not A got merged into A just fine. But if a pic was in both catalogs, its master in A had its metadata replaced by the "empty metadata" from B, with a virtual copy being created containing the original metadata. Worse, that master has been removed from the collections it was in, replaced by its virtual copy.
To avoid this, why not just select the option Replace: Nothing? That way, only pics in B that aren't in A will get imported into A.
If my understanding is not correct, then please elaborate on the scenario, using the same terms (A and B).
You are absolutely right. That would be the best thing to do. Unfortunately I have done some work on it already which I didn't have a back-up for.
In the end I went for option 4. A big workaround but it only took a day, so not too bad.
I should've definitely make a catalogue back-up before merging... Learning the hard way!