Usually the files on one drive will not transfer to the other drive without you executing a command to do so. Most spyware files are in the registry anyway, and that is not a likely file area to be transferred to your other hard drive. (I take it you have an extra drive for storage of media,.etc...)
Spyware and viruses also usually need an operating system structure to spread and do what they are programmed to do.
The key words here are "usually".
It is always best to clean an infected drive asap, to ensure that your data stays intact, and does not spead to other drives or computers on a network.
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