I have two SSD, HD's. One has Linux on it, the other Windows. I installed each system on the drive by itself, with it being the only HD. Then put both in, with Linux first. I updated grub and have been using a dual boot with each OS on it's own drive, using ASCI.

Cleaning up, I found an old ide HD. I took out the Linux SSD, put in the bare drive and installed a different distro on it. Used it for a week, then took it out and installed the linux ssd back in.

When I go to boot to windows, It cant. I checked and found the BIOS is set to ide (I never changed anything). I put it back to the original ASCI that the drive was installed at, and it doesn't work. I put it to ide, it works.

Linux HD boots in both, but Windows (ssd) only boots in ide.

How did this get so screwed up?

Any input or explanation that would help me understand what happened and how to fix it without doing everything all over again?

Thank you,
Chris.

When Windows didn't see an AHCI drive it uninstalled the driver. To fix that, leave the Windows drive in IDE mode, but install a second drive set to AHCI mode. When Windows sees the AHCI drive, it will install the driver. You can then configure the Windows drive in AHCI mode, and all will be well.