Before you do anything, back up your catalog. How to back up catalogs in Lightroom Making a new E: partition won't buy you anything, you have to untangle the mess caused by the synch: "The Dangers of Synchronized Folders" https://www.lightroomqueen.com/synchronize-folder/ If I'm understanding correctly, 16k images of your 42k were seen as missing, and so "duplicate" entries for their new location were put into the catalog. I'm not sure why it was only 16k. I think your next step is to try to intelligently ascertain whether all your files were restored retaining the old file structure, or whether they became divided. Hopefully with more information we can see if you can delete these duplicate entries easily, and then easily relink your previous good catalog entries by pointing to the topmost pertinent folder in the catalog Lightroom – Relinking Folders on an External Drive « Julieanne Kost's Blog (ignore "external drive" in that discussion - your C: drive is your new "external drive, if that makes sense) I know this is confusing, but if you can sort out and easily remove the duplicates from the catalog, you might be halfway home. Also, I'd wait for others here to confirm my approach or suggest something better/easier.
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