FIx RAID configuration after upgrade to Debian/Jessie with ICH9 chipset

I upgraded from Squeeze to Wheezy without problems. But after upgrading to Jessie the system cannot boot anymore (using LILO). LILO ERROR: Duplicated Volume ID O 24.1 Loading Linux ....(snip) BIOS data check successful Loading, please wait [ 14.948425] end_request: I/O error, dev fd0, sector 0 mdadm: /dev/md3 has been started with 1 drive (out of 2). [ 27.196906] end_request: I/O error, dev fd0, sector 0 ...snip modprobe: module unknown not found in modules.dep fsck from util-linux 2.25.2 mount: mounting /dev/root on /root failed: No such file or directory ...etc. And i get to the (initramfs) prompt When I try to list partitions of one of the RAID disks they don't show up. (initramfs) ls /dev/sda* /dev/sda Examining the disk says (initramfs) mdadm --examine /dev/sda /dev/sda: Magic : Intel Raid ISM Cfg Sig. Although the onboard RAID controller is disabled in BIOS. When I access the disks with KNOPPIX (7.0.5) I can access and sync the partitions (sda1, sdc1) without problems. So I guess: * The RAID disks have been created some time in the past using the onboard RAID controller * Because debian didn't support ICH9 chipset the support for this was disabled in BIOS * Jessie seems to look not only at the superblocks of the partitions but also on the superblocks of disks and fails because they are identical? How should I fix this problem? * Enable ICH9 raid in BIOS resync the disks there? Will the system boot? * Zero-out the superblocks using mdadm on the disks