"Unknown pack version"
I checked the files you mentioned and the windows version of avast doesn't have a problem with them (strangely enough?).
The files are packed with the Inno Script Studio (software to create installer packages).
I don't know for sure, but it can be that has something to do with it.
Most windows install packages are created with InstallShield or NSIS.
About the number of files/folders, I have no clue.
Well almost no clue
Perhaps it has something to do with scanning a windows drive from within Linux and/or because it is a external drive.
If it is a 3 Tb drive, at least the size is reported correctly.
I would not worry too much about the files/folders if the size is correct.
I don't know if someone from avast or someone who knows more about this issue will respond before you go scan your friends drive...
But to me it looks like you can do so without a problem.
Alternatives are:
- hookup the drive in a clean system as slave/second drive and scan it.
- hookup his system to the router (if you have one) and scan over the network.
- create a bootable cd/dvd with windows and put avast on it and scan from that.