Thank you for the only useful reply. Talked to some other people on the issue and they said the same
All that these fine gentlemen said is true, it's simple physics which nobody can argue about, but (a big one) the effect of removing one hash board isn't exactly that huge, the impact on temps isn't all that bad, the two boards will run cooler if a 3rd dead hashboard is there (better airflow + the heatsinks on the head board will absorb some of the heat from the other working hash boards), but the two boards will still run cool enough regardless, they do get less airflow compared to a full miner, but the heat that was generated by the 3rd board is no longer there which helps to balance things out.
I tried that on tens of S9s, the effect on temps is little to nothing, nothing major that had me modify anything, so really, the only way to know would be to test your miner, do a before and after test, I highly doubt the temps will vary widely, but just to be safe.