No problems, let it running at night! 8)
I think it does not freeze when avast! is well installed.
I’m not sure what files will be skipped but, really, time is not a problem when you are infected.
avast! does not fragment your drive! It just unpack archives (like .zip ones) and scan the files, after that, the created files are deleted. The original file does not move in the HDD.
Hope this help. 