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What type of computer and operating system version are you using? Exact version # of LrC?
Did this operation remove all virtual copies in all of your folders or just the folder you synchronized?
I just gave this a try on a folder that had one image that wasn't in LrC yet. The virtual copy I had in that folder along with the not yet imported image were there after the folder synchronization.
The first thing I would do in this situation is reset LrC preferences. That is a good thing to try anytime LrC starts doing strange things. I am on a PC with Win 10 and LrC V 11.1
Also, be sure your catalog is backed up through the LrC backup, checking the integrity and optimization.
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Use a backup of your catalog file that still has the virtual copies.
I haven't tried Synchronize Folders with virtual copies, but Synchronize Folders will remove files from Lightroom Classic that do not exist on your hard disk in that folder. My advice is to not use Synchronize Folders without being 100% sure of the repercussions.
As far as your non-destructive comment ... Lightroom Classic doesn't do destructive things unless YOU the Lightroom Classic user, gives a command that causes destruction. Then you get destruction.
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FYI-