Sounds like you have overwritten your series 1 backup with your series 2 backup.
The backup command specifies the filename - eg. /mnt/dos/tivo.bak - so if you want to save separate backups then you need different filenames - eg. /mnt/dos/tivoS1.bak and /mnt/dos/tivoS2.bak
And no, you can't use the same backup for both machines as S1 and S2 machines are very different, so at this point you need to rename your existing tivo.bak to reflect the fact that it's from your S2 machine and then redo the S1 backup to a different file.
6023, Lifetime, 240gb, Sky, CC, Mode 0, 100 SPs/AWLs
6022, Lifetime, 250gb, Freeview, CC, Mode 0, 90 SPs/AWLs
601E, my 'test' machine!