OS3.9 doesn't "hide" any files to access beyond the 4GB barrier. It patches scsi.device (if you use it) and FastFileSystem so you can use devices larger than 4GB without experiencing the "wrap-around" effect.
The safest thing to do would be to boot from a Workbench 3.9 Emergency Disk and your OS3.9 CD so you get all the ROM patches, then use HDToolBox and Format on the OS3.9 CD to create and format the partition. Then run Quarterback (still booted from the Emergency Disk) to restore your backup.
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moto