Chkdsk is really just about correcting
system indexing errors, identifying weak sectors of the HDD, writing anything there somewhere else and marking the weak sector as not for use. That's about all it does.
It should repair any faults in the system indexing caused by malware but it isn't going to re-activate deleted malware itself.
Doing something like that sounds like the sort of bad idea a book author or screenplay writer might use as a plot device for re-infecting a computer or network.