As I don't have physical access to the server currently (I'm remote accessing it from work), I did extra troubleshooting as below and it's working again.
Changed the drivers to LibreElec -> reboot = didn't work
Changed the drivers to TBS-OpenSource -> reboot = didn't work
Deleted the plugin -> reboot -> downloaded the plugin and changed the drivers to TBS-OpenSource -> reboot = WORKED!
However, I guess your statement regarding the controller chip is correct. Before using your plugin, I used to passthrough the cards to ubuntu VM and sometimes the cards doesn't load after reboots. However, changing the "PCIe ACS override" VM settings and getting them back again to what I need them to be solves the problem. Or maybe just a bug in unRAID 6.9 rc2.
Again, I'm not an expert here and just guessing. As usual, thanks @ich777 and apologies for jumping to the forums without taking the extra mile of troubleshooting, but hopefully it will help someone who is facing the same issue or helps someone to figure out what causes the issue.