I recently added an LSI SAS 9300-16I 12GB/S HBA BUS ADAPTER CARD IT Mode 4*SFF-8643 SATA Cable to my unraid server. It replaced two 8 port HBA cards. When i added this it caused my motherboard sata ports to go glitchy sometimes 4 would work so 5-6 didnt work other times 1,3,5 worked and 2,4,6 didnt work. I ended up using an old HBA with the new one and all drives were detected. This is my motherboard MSI PRO Z790-P WIFI LGA 1700 Intel Z790 SATA 6Gb/s DDR5 ATX Motherboard once i swapped the 2 HBA for 1 the sata ports have not been working the same. Any thoughts on what could be going on? My power supply is a 1000 and had no issues before swapping HBA cards. When i loaded into unraid I was missing 4 drives

This usually is the "HBA in the wrong slot" issue.

Many modern motherboards are "overequipped" which means, you cannot use all installed devices at the same time. For instance "if you use Slot #3 SATA 5-8 will not be available anymore" or other complicated stuff.

Only the manual for your motherboard can tell you about these restrictions, look for (*) footnotes.

 

I guess, your new HBA claims 8 or even 16 PCIe lanes for himself, Mobos usually offer only ONE slot (the first, meant for graphics adapters) for these kind of devices.

Also, look closely at the slots! Even if they may look "large" there are often not all lanes available (no contacts there, its visible!).

 

You may end up swapping around cards to create a stable an working system again. Or, you may find out that your desired combination is not possible with this board.