Help for Acer reformat

Hello,

Long story short
Okay, I'm helping my friend reinstall to get rid of malware.
I notice he has two disk drives each with 228 GB of hard disk space.
I assume it's a mirror of the operating system on a 2nd hard drive.
I format the 2nd hard drive
I start copying personal files over to 2nd hard drive
I start the Acer eRecovery process, which I assumed would be just like a regular reformat where I would delete the main hard drive's partition and reinstall the OS.

I was wrong. Acer's eRecovery started doing it's own thing.

Later I find that it's not two hard drives, but one hard drive split into two partitions creating a 2nd "virtual drive."

Now I am worried because my friend has personal files on that 2nd partition.

Acer's recovery disk should not be able to find the mirror files on the 2nd hard drive becuase it's formatted.

But will it reformat that partition and get rid of my friend's personal files? or skip over it because it can't find the files needed to continue?