There definitely *is* still a partition size limit with FFS, but I am not sure what it is. I *think* it is 8GB for 512 byte blocks. So for a 50GB partition, you have to use a block size of 4096 bytes.
But at first I agree with Piru. If the RDB got wiped, you're not using the right software for big HDDs.
Which Format program did you use and did you do a full format or a quick format ? 64bit support was first added to Format with BB2, IIRC, so you have to use the Format program from the BB2 installation in order to fully format any of the big partitions. Quick format should work correctly with all versions, though.
1GB( for Debian;)/
I'd create a 1GB swap partition and a 10 GB root partition at the end of the HDD. The Linux kernel knows well how to deal with big HDDs and the Linux launcher has to be run from AmigaOS anyway. So you can install the launcher on your AmigaOS partition and have the Linux partitions above the 4GB line without size limit.
All important data should be stored above the line, either. Because *if* something happens because of the 4GB limit, the area *below* the line will be hit, never the area above.
Bye,
Thomas