After rebuilding de BCD, apparently it was found as an actual OS again. From there on I could fix startup issues in the troubleshoot section of "Repair my pc", which resolved the issue entirely. I still have no idea why this happened, but if anyone ever for some reason runs into this issue:
- Make sure that the main boot disk is on top in the boot priority tab
- Boot from the CD
- Go to "Repair my PC"
- Open the terminal in troubleshoot
- Run these commands:
- bootrec /FixMbr
- bootrec /ScanOs
- bootrec /RebuildBcd
- Restart the VM and go to "Repair my PC" once again
- "Fix Start-Up" should now work, and after that, the VM should boot again.
Thanks continuum for the suggestions, they got me further:)