Factory restore without losing my backup partition

Hi ya'll.

I have a 3-months old laptop, and it's been driving me insane recently - touchpad is freezing, windows losing focus, apps and games crashes and it's mainly just working really slow, and not in the way I would expect from a 3-months old laptop with a configuration that should be running Windows 8, some internet-surfing and videos with no problem.

I decided to do a factory reset using the recovery partition and just start fresh.
Now, I'm a student abroad and I'm on vacation now and left my external hdd back at my place where I live during my studies. In order to backup everything I needed (roughly 95 GB), I shrunk my C drive by 100 gig and created a secondary partition, and just moved my files there.

Now when I came to restart my laptop to start with the process, I realized it says all my files and data will be deleted. I haven't done many factory resets in the past but if I remember correctly, unlike windows disc-installation, it won't let me choose which drive to format and install the new OS on, it'll just delete everything and restore it to the state it was in when I first got it.

Since both drives are on the same HDD, will it actually be deleted? (the secondary drive).

What can I do to "tell it" not to touch that drive?

Thanks!