I'll say it again:
Replace The Backplane with Wires
As in 1 (one) SPI channel PER HASHBOARD going direct to a controller. I hope to god you didn't have all the hashboards sharing a common bus on the backplane before - because I can't imagine trying to get that to work.
Unfortunately, I think that BA really did try to create multiple SPI control signals on a single SPI connection across the backplane. There really is no other explanation for why "SPI communication" fails with more than one hash board. If they used independent control wiring (one to one) rather than an SPI bus approach, then what BA describes would be impossible:
"The issue is the SPI communication fails on the current backplane as soon as you attach more than 1 hashboard."
I cannot think of any explanation for that behavior unless they attempted to have SPI "one to many" control to slaves. As the beginner's guide to SPI points out, that way lies ruin.