Avast told me I had trojans. Did the quick scan which found files, then did the boot time scan. MANY MANY files found. Many couldn’t be repaired, moved, or deleted. At first I just hit ignore, but there were so many, I hit ignore all since I figured it would only apply to those types of files. Well, duh, now I’ve realized that Avast is probably ignoring many infected files. :-\
Advice?
Update virus definitions.
Rescan files into Chest (right click them).
Restore the clean ones.
Run a full avast scanning.
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.
Thanks. Since I posted that, I realized it was the problem with the update, so I’m good. I found the files in the virus chest and restored them. They weren’t that many considering how many I deleted during the boot time scan (html files, I guess) before I chose ignore all.
I feel much better, I think! 
Direct deleting is not the better option, ever…
Whilst most of these html files will have been in your temporary internet files folder, some could well have been in other locations. But there is a lessor risk of harm at the lose of an html file than having opted to delete sat and .exe file.
So it really is a lesson in exercising, first do no harm, don’t delete. Move to chest and investigate, but if there are multiple detections you should be looking at what files are being detected for a common file type and malware name. Then you should consider stopping the scan and investigate what you know about the existing detections.
Check the avast forums, avast blog, etc. and see if there is anything listed that day.