If you save the bios setting changes you made and keep power cord plugged in, you should be able to see the changes stay after restart.  Are you saying your changes do not stay after restart (and do you keep power plugged in during this)?  If you have only one hdd in it, it really doesn’t matter what sata mode you have (AHCI vs IDE), I think.  As long as OS on hdd can boot, it makes no difference.If you had soldered a new bios of board, the motherboard might be altered (my guess).  I would not change motherboard, definitely not in a DT.  If you can still use it just get the most of its remaining life.
Hello, Waiting for response ASAP. Note:I know it is 12 years old PC so please only reply if you have solution. 
Optiplex 780 not booting up until pressing back psu test button