DavidR
3
Personally I have never had this happen to me.
But if this did happen the first thing I would be thinking would be probable false positive, pause the scan and collect some information, url and or file name, location, malware name, etc. and if these were not on .exe files (which could be a file infecter and quickly effect many files) I would stop the scan.
So personally I don’t think that you have made a big mistake, given there was an FP in one of today’s virus definitions updates, https://blog.avast.com/2011/04/11/false-positive-issue-with-virus-defs-110411-1/. Once this was discovered, all update servers were blocked to prevent more people getting this update. This was promptly corrected in version 110411-2, released to the update servers and they were unblocked. But with 125 million active users it still effected a lot of people.
So ensure that you have the latest update, reboot and scan again, but not a boot-time scan where you have less control.