Can they even tell the difference?
They can, and by doing so, you will void the warranty according to their reply to your question, you could still ask them, you lose nothing.
i think
"If the hashboard is sent separately, the whole machine can not be debugged. It is possible that the repaired hashboard can still not be used after being installed. The warranty will be lost if the hashboard is sent separately, If you accept this risk, you can send it separately"
mysticbitcoin, the problem with that you did is that you changed two aspects at once, now the results may be very misleading, was the bad board causing the issue, or was it the psu? you removed the hashboard and replaced the PSU, the logs changed, in the end, the results are not satisfying, kindly put the bad hash board back and keep the new/working PSU.