Mac Pro not detecting internal HD. Blinking Question Mark!!

Hi there,
Ive been looking for an answer about my problem but it seems most of the people has got the problem; the hard drive might be damaged. Thats not my case.
Ive got two Mac Pros. One is working flawlessly. So I swaped HDs to see what happened and when I turned on the computer, the good MAC detected the hard drive of the failing computer and I logged in normally. When I turned on the failing computer with the good HD, it didnt read it. In conclusion I realized that there was not a HD problem, something else is going on.
After that, using the good Mac PRo, I installed both HDs and both were detected. This confirmed that definitely, the HDs are Ok. Whats wrong?? I dont know, hope you people can help me.
Thanks a lot.

The blinking question mark says you could not find:
The preferred System
of the preferred version
on the preferred drive.
All these parameters are stored in Parameter RAM, and sometimes they get damaged "just because".
If you use
System Preferences > Startup Disk ...
... to set the correct startup disk again. your problems may be over.
If not, you may need to reset the PRAM.
If that does not solve the problem in the long run, you may need to replace the PRAM backup battery.

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