If the sata controller was in raid mode with two drives and a Windows install then that windows partition was probably spread across both drives...
Have you tried booting windows to see if it's still intact?
Fwiw, I have a 990 running High Sierra / Mojave and legacy mode is the way to go for the bios, Clover will load and then boot the UEFI Mac partition. AHCI mode is also required as far as I can tell.
I installed Windows when only the SSD drive was in the 990, so the OS should be on one drive, but I guess the SATA controller was set as RAID when this was installed. Not sure why, likely it was because of RAPID STARTING technology (that's what's indicated in the RAID line when selecting it. Now when I boot the 990 up and the SATA is not in RAID mode, Windows doesn't boot.
After the Mac OS X install/reboot, the Windows Os was "damaged" but when I went through a reboot, it repaired itself and started back up. It's working.
Now, in Windows 10 disk manager, I can see the SSD and the HDD with Mac OS X (Legacy Bios, RAID SATA)
The Win10/SSD has;
1) a 39 mb Healthy (OEM Partition)
2) a 368.06 NTFS (System, Boot, Page File, Active, Crash Dump, Primary Partition
3) a 513 MB FAT32 (Primary Partition)
4) a 97.16 Gb Healthy (Primary Partition)
I think #3 and #4 are the Ubuntu portion, and #1 maybe something to do with Samsung SSD, and #2 is Win10
The Mac OS X/HDD has
1) a 200 mb "Healthy (EFI System Partition)", EFI I'm told is same as UEFI.
2) a 465.57 Gb "Healthy (Primary Partition)"
I was thinking that's causing a problem! So maybe redo the install with the UEFI configured UniBeast software?
Then should things be magically fixed BUT still may have to select ACHI SATA mode, and UEFI boot mode to get to the MAC OS X?
Or delete the 200 mb EFI partition, repartition, and format, and re-install the Legacy Bios version?
Not sure. I'm a little disappointed because the Boot into Mac OS X looked perfect until after MultiBeast reboot, thinking I could have left it? NOT!
If you have any suggestions, I would appreciate it. I just re-mastered the USB in UEFI mode, and was going to try it, but I'll see what you suggest.