Hi,
I don't think that swapping the CF cables would cause any harm - you would just map slot 1 to CF2 and vice-versa.
Unless, of course, you put the flat cable the wron side around, which again I don't think is an easy thing to do...
You might have:
- broken HDD
- corrupted file system
- broken module
Or, and this is a long shot: because you connected the CF slots in the wrong order, the C, D, E, ..., letters are now messed up and the BIOS/filesystem tries to load files from the wrong unit?
Good luck!
Regards,
Vitor