Work of scaner mostly depends on it's type - SCSI/LPT/USB/..., because TWAIN-interface is supported. Also you can find information about scanners and OS/2 here.
How to prevent data loss? a) don't use old version of JFS driver. b) Don't boot from old eCS CD1 (if you take eCS 2.0 CD1, then disable its disk checker else it can kill your partitions), Advice how to use JFS filesystem