I don't think boot scanning will do it, as I believe that file is part of windows directly, as such it will already be in use by windows before the scan can start.
What you need to do is be able to scan it with out windows loaded or running (that way it cant lock off anything). This is also how one gets around viruses blocking removal.
You also may want to run chkdsk as well to make sure its not a problem with the drive itself.
As far as I know though, viruses don't target that file (they usually go after dlls, executables, and installers). So you could just add that file to the ignore list of Avast, and finish the scan (assuming it has an ignore file list).
Anyhow it looks like the normal avast doesn't offer a boot disk virus scanner (has to be purchased separately or you need an advanced version of the software). So if its simpler just wipe and remake the partition (format it, or if your paranoid, delete the partition, remake it and then format the new partition etc)
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