Check the bios for a delay in boot time.  I have some boards that let me set up to several seconds delay before boot.  Ive always used the longest delay to allow the pcie bus to read all cards on my 13 gpu rigs.  Hope it helps you.

I'm not aware of any BIOS boot delay, just the bootloader which has nothing to do with HW detection.

I think there's a problem that requires troubleshooting. The problm is intermittent and affects GPUs randomly, the most difficult to solve.
My first suspicion is the PSU. If you have a spare, preferably a bigger one, give it a try. If not try removing one GPU to reduce power and see if
the problem goes away. If it's not a power issue then you're looking at a possible BIOS/motherboard issue. Updating the BIOS may help.
Shuffling slots and risers can also help make problems mysteriously disappear, sometimes a shuffle just reveals a pattern that leads in one
direction.

Regardless a better workaround would be to count the GPUs after reboot instead of relying on hashrate to detect a missing GPU. There are many
ways to do it from a command line or BAT file.

Had a similar problem a while ago. I made a script (batch) that first checks, how many GPUs are in the system ("PhoenixMiner.exe -list > GPUS.TXT"). You then can analyze the GPUS.TXT file how many GPUs are available and compare it to the number of GPUs that should be there. If its okay, then start Phoenix with the normal parameters, otherwise generate a shutdown/restart.

It's just a workaround but it did what I wanted :-) Maybe its a way for you also to get the problem solved. Anyway you should try to find and fix the problem itself...