Whether they are repairable depends entirely on what they are. System files affected by a virus sometimes are. Trojans/malware executables are not; they are malwares in themselves.
What are the infected files? (Names/paths)
Will do no harm to leave them in the chest; they won’t escape.
Given the state of the machine, it might pay to download http://www.superantispyware.com/ (free or paid) (works with '98) and scan with that, too.