I had another disk/partition adventure recently. My notebook stopped booting after I updated XUbuntu on the second partition of the HD. Apparently the update screwed-up boot sector on Win XP partition (the first one). So I got a USB flash drive with WinXP SP3 setup and booted from it hoping to use Windows recovery tools: fixboot and fixmbr. Unfortunately the recovery was not able to find any Windows installations; in fact it did not see the disk at all. The notebook uses Intel ICH9 controller and its drivers are not available on the setup disk. Apparently I could not use a floppy to add an extra driver in the boot process, so I needed to add these drivers to the installation. There are instructions on how to do this using nLite, but it looked like it can take a long time. And then I realized that I can disable AHCI mode of the SATA controller. One change in the BIOS settings, and the setup disk could find Windows partition and I fixed boot sector using fixboot. After fixing the boot sector I changed SATA controller mode back to AHCI and everything worked fine.

On other motherboards/notebooks these compatibility modes can be called differently (ATA, IDE, something else?), AHCI is sometimes called “native” mode.