window files infected...what to do?

:o When doing the boot scan I had a few window files infected with either trogan or worms, i moved them but why did it ask me if I was sure I wanted to? Should I not have. If I had deleted them would that affect the running of the window application on my computer? When do you know if it is safe to delete a file on the boot scan?

Let me guess. The files found where in the windows folder, right?
Not everything in the Windows folder is part of Windows.
Many applications are also placing files there.
Many malware (viruses, trojans etc) are also placing files there.

Leave them in the chest. If you don’t experience any problems the next few days with your system, delete them.

Most probably you won’t be able to move the infected files to Chest at boot time because the drivers were not loaded at that time…
Move the files to a known folder, after boot and logon, run an on-demand scanning of avast and send the files to Chest.
Hope this helps.