So does the whole FILE go into the chest or just the virus?
The whole file.

Files infected with a real virus can be repaired, other malware can’t and requires files to be deleted.

hould have have a clean spare copy of the virus infected file
It is always recommended that you backup on a regular base.

And Avast has the VRDB

VRDB stands for "Virus Recovery Database"; it was known as "Integrity Database" in previous avast! versions. The aim of VRDB is to help when, despite all the security measures, a virus gets inside the computer and the files are infected. With the help of VRDB, it is possible to repair infected files (return them exactly to their original state). VRBD is announced by an icon with the letter "i" in the system tray (next to the clock). If the icon is animated, the database is being created right now.

VRDB PRINCIPLE

avast! creates an integrity database, i.e. it stores information about the actual state of the files, doing it three versions back for each file. The database creation/maintenance is performed either when the computer is idle, or when the screen-saver is running (any screen-saver, not only the avast! one). This database, once it is created, is updated each three weeks (this value may be changed by editing avast4.ini).
If any file is infected by a virus, it is possible to repair it, i.e. turn it to its original state. If there are multiple versions of the file in the database, you can choose which version you want to restore.