Will a clean USB install touch the 2nd hard drive of a mac mini server?

I have a late 2012 mac mini server (16gb) with two integral factory drives.

The second drive contained only virtualbox images for playing w/windows.

I have updated Everything on Yosemite to be current as of today, rebooted, then turned on TimeCapsule.

I then directed TimeCapsule to use the second hard drive and allowed it to complete the 260gb+ backup.

I want to do a totally clean install of El Capitan via USB- and am about to follow the directions to a T.

I have a question before I start. WILL the USB Clean Install method touch or alter the second hard drive?

I do not want to open the aluminium case of my macminiserver/muffinwarmer to be assured it wont erase the second drive.

After installing El Capitan, will I be able to use time capsule to recover the added programs, user logins, photos, iTunes library and playlists, and other data from the added programs in a single simple step?

I bought this to be stable and reliable. So far, so good. I need expert help only occasionally and this is one of those times.

If i DO need to temporarily remove the 2nd drive, id like merely to a disconnect power or data or both cables instead of removing it entirely.

I have the server mounted on an suspended and damped earthquake proof fixture located far from any known faults "just because".

It's powered by a UPS powered by sled dogs and a lead cat.