One other thought: would there be some way to add copies of some of the files in a virtual file collection into another and only add ones that are from new files (to avoid the above mentioned problem of finding he duplicates)?
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The following steps worked for me:
1) Highlight your desired collection folder
2) Go to Library mode
3) Using Lightroom dropdown menu choose Library -> Enable Filters
4) Then choose Library -> Filter by kind -> Virtual Copies
5) In the film strip or the tiled view, select all (command-A)
6) Then press delete.
hannahb26810959 I had the same question as you re- virtual copies. I think I found a way to eliminate all virtual copies in a collection and posted it as an answer to your original question. Please try it and tell me if you can replicate what worked for me. Thanks.