The kernel panic certainly isn't a good sign. It looks like the software is waiting for a certain status from the FPGA which doesn't arrive.
[ 785.178931] [000010c4] *pgd=00000000
This means the CPU tried to access memory that isn't mapped, could be the equivalent of a null-pointer de-reference.
The stacktrace is also a bit weird, it failed in sched_show_task(), called from rcu_print_detail_task_stall_rnp(), this is a standard diagnostic kernel function that belongs to the RCU subsystem (read-copy-update). It appears the kernel detected a stuck task and tried to call it out and then panic'd while it tried to print the task data.
It sounds like there's something very wrong, at least something that the software was never prepared to handle sensibly.