It’s been a long time since I last installed Linux on a two hard-drive system, so take this advice as “likely not necessary, but will probably fix your issue”
The installer asks whether or not you want to “replace” the existing OS or install alongside. And if you’re fairly new to linux (like I was at the time) it can be tricky to see at a glance which hard-drive you want to install it to and which you don’t.
So to be doubly cautious and make sure that didn’t happen, I simply unplugged my secondary harddrive during the install so that the installer would automatically be reading the correct one. Then all I had to do was choose “replace” or “install alongside” without worrying about anything else.
The drawback to that was, once the install was complete and I re-attached my second drive, I had to configure it to auto-mount and do some work on that, but at least my computer was working.