File systems, do they matter, huh and what happened to my data?

[spazzy]

I have two external hard drives which I sync together with SD. The source drive (HD1) is formatted with mac os extended (Case-sensitive, Journaled) the destination drive(HD2) is formatted with mac os extended ( Journaled).

I synced today between the two and right after accidentally blasted a bunch of stuff from my source(HD1). I used smart copy to sync my source(HD1) to my destination(HD2) but I noticed two strange things

1) my source drive(HD1) has 10G extra data than it should which really confused me so I sync HD1-->HD2 but still HD1 has more data (number of files and drive space used)
2) A bunch of random files are missing from both the HD1 and HD2 drives


what gives?
I can only guess this is because the file systems are slightly different?
Each time I sync it was with smart copy.

[dnanian]

You definitely shouldn't copy a case sensitive drive over a case insensitive drive, because you can have files that can exist side-by-side on the source but not on the destination (e.g. files with the same name but case differences).

But, certainly, we never touch files on the source except to read them. If you're missing files on the source, it happened outside SuperDuper.

Not sure why your source would have 10GB 'extra' data. Is it your startup drive?