I haven't had any problems with large files going back and forth between
the file systems but I have seen using "mv" within a dos filesystem
corrupt the filesystem and lose the file every time.
eg: mv /dosd/something.gif /dosd/pics/

The only way to fix the file system seems to be booting to dos and using 
chkdsk or scandisk.

Of course the file I wanted to move is nowhere to be found, not even lost 
clusters.