Edit: I fixed the problem with EasyBCD eventually.

I recently had problem booting due to system reserved partition tinkering and had to install a second Windows 7 to HDD in order to boot and fix the system reserved partition. The original W7 is on the SSD and everything is working fine, if I open msconfig the boot tab tells me I only have one OS, but the windows folder in the HDD is clear as night.

Now I am preparing a full disk encryption, it asked me wether I am single boot or dual-boot. I assume clicking single boot will work fine, but this is a good time to get rid of the second windows.

I've seen solutions online where formatting the HDD is part of the solution, I don't have the resources to backup 1TB. What are my options?