As Equill suggests, suck it and see. The 50 pin IDC is SCSI II, so if your pin identification is correct, it should work. If your pin identification is wrong, via any incorrect orientation, it won't work.

Assuming the worst, and that essential pins are missing, how easy is it to remove and replace the IDC header? De-soldering 50 pins is not to be taken likely, but are there any other potential problems?