I ended up solving the problem by installing an internal 2 port SATA card. Thanks for the replies.
Precision 3620 i5 8gb ram has latest BIOS. Its got the 365 watt 80 Plus Gold power supply and the stock NVIDIA Quadro K420 2GB video card. This PC is the family's camp media player and I have had it set up to run Kodi and media stored on 4 internal 3.5" HDD's for a couple years with no issues. Its not used for anything other than Kodi audio and video playback, no internet or cable or phone service at camp, I just brought it home for the season and the HD with the OS and some of the media was nearly full. I figured since I would have to migrate the OS (windows 10 Pro) to the new larger drive I might as well just install a SSD in the M.2 slot and be done with it. I installed the M.2 SSD with a fresh load of windows, I also installed an internal 2 port SATA card because I figured the M.2 would disable at least one of the MOBO SATA ports. Boots fine, Runs fine but now the system only finds 2 of the 4 HDD's. it does not matter if they are plugged into the MOBO or the SATA card. its almost like the PC has disabled the power supply connectors for the 2 not seen, but its one drive on one of each end of the 2 daisy chain connectors and it does not matter if I reverse which HDD is first in the daisy chain from the Power supply. Its weird, I can take the drives out and put them in an external dock and they work fine. I would rather not have them out of the PC because about 30 people in the family share the camp so its just something else to get broken when I'm not there. I'm sure its something obvious and i'm just thinking in circles but I cant for the life of me figure out what I have done wrong.
Precision 3620 installed m.2 ssd and lost 2 internal 3.5 drives