I finally got around to updating my machine from 10.12.4 to 10.12.5. I had updated a couple of others already and had no issues, so I expected this to go smoothly, but not to be...
Motherboard: Gigabyte GA-Z77X-UP4 TH
CPU: Intel Core i7-3770k
Video: Nvidia Quadro K2000
--- Feel free to skip to the end/solution, I'm realizing this tale may not be as interesting as I thought as I type it, but I've gone this far ---
I have used the same Clover config and hardware for a number of years with almost zero issues. After the update, the machine restarted, but part way through the boot process (Apple logo + progress bar), the screen would go black and there would be no video. I could boot in safe mode, so I made sure the update installed properly, which it did. Tried a few more reboots with same results. I updated Clover, since I had not done so in quite some time, but no luck. Also tried a number of different Clover options, installed the Nvidia web drivers and still the same behavior. There were no issues booting into Windows.
I then dug out an older video card (GT 240) and swapped out my Quadro. That booted ok. Then I put both in together with one monitor connected to each. The machine booted, but only the monitor on the GT 240 worked. In System Information, I could see the Quadro listed and all of the specs looked fine, but no monitor was shown connected. Somehow the machine was recognizing the Quadro, but not any of the outputs. After monkeying around some more (NVCAP, and some other things), I tried a different SMBIOS model (from iMac12,1 to MacPro5,1) in the Clover boot screen. That booted fine! So I thought I finally had the fix. I updated my Clover config to MacPro5,1 (keeping my serial number, board ID and board serial number) and restarted. Back to the blank screen.
After more messing around, I found that if I go into the SMBIOS config during Clover boot and edit the model field, just pressing enter twice (but not actually change anything), it would boot fine. So forcing Clover to react to the change caused a successful boot. Seemed that it needed to do something with the SMBIOS information, not just load it from the config. Next order of business, I removed the entire SMBIOS section of my Clover config and restarted and the machine booted fine. I added only the 3 fields back, left the rest blank and restarted; black screen again.
--- end/solution ---
I re-edited my config.plist, removing the board ID from my original config and got my Quadro back working again. Letting Clover auto-generate that (if it is indeed needed) has been reliable so far (possibly better? Seems sleep/wake/restart is a little faster now...). It has been so long that I had been using the same SMBIOS info (with success), it took me a long time to question and start changing those parameters. It is unclear to me why, after so many updates and rebuilds, 10.12.5 had an issue with the board ID, though.
I hope this may help folks looking for answers after the 10.12.5 update (or maybe others).