A couple other sync programs have a feature were you can select that the sync aborts if certain percentage of even number of files has changed (think ransomware etc)
Does free file sync have this feature?
Detect if 50% of the files have changed and abort sync
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It does not have that feature. There is a pop-up if two locations are significantly different, but that is probably hidden by every user ever
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FreeFileSync already has this function, but it's a warning, not an error: "WarnSignificantDifference"