Missing File Manager :
1:
After clicking RELOCATE button (with multiple files selected), add prompt to select a folder on the storage device. Have a tick box for "search all subfolders"
2:
When the located file already exists elsewhere in the database (because 2 copies of same tune existed, and one was deleted), prompt to choose to "merge the two file entries as one". The missing file will be replaced by the existing file throughout the database.
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In the meantime, I wrote a workaround tool which might help:
Main page with installation and usage instructions: https://github.com/edkennard/rekordbox-repair
Page to download packaged version of the tool for Mac or Windows: https://github.com/edkennard/rekordbox-repair/releases
Hope it helps :)