I'd like to reformat the disk and install a fresh version of OS6 for my Plus. Is their any (hard or software) way to do that or does the interleave issue makes it impossible ?

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Decent third party formatters that will run on your 6400 will allow you to specify 3:1 interleave so that it will be usable on your Plus. However, the drive will be unusable on your 6400.

A better solution is to download the four 800KB System 6.0.x floppy disk images from Apple and create some real disks. Use the HDSC utility on the Disk Tools floppy to format the SC20, then reboot from the Install floppy to install System 6.