True. While the system is booting up, the files run would be scanned by File System Shield, so is possible changing settings in File System Shield from automatically quarantining in this case to ask, in this case, would allow some control over an erroneous vps in place or file rep issue that somehow manifested itself here. That is all we are after here. These changes in settings are not for the average user, as most would not know how to answer and choose the right choice in action.
To summarise, normal actions are as follows: Quarantine, then delete. Deletion is to be avoided if at all possible, as once that is done, the file is gone forever. Repair only works on normal files that are infected with a virus.
Repair cannot work on trojans or worms as the entire file is an infectious agent, so there is nothing to repair. A virus infection is the result of a normal file having a part of its' code overwritten or changed to suit the intended actions of the virus code, so removing the virus code will, in most cases, clean the infected file. A windows system file can be controlled/renamed by a trojan, and deleting a needed system file will wreck havoc on a system to the point where it may not boot again. So, deleting is the very last resort, and is best reserved to remove known trojans or worms. An infected system file can always be replaced by a known clean copy.