That is a known issue with the fog of war in the battlefields.
I don't know why chkdsk would freeze on files/folders that are fine on the hard drive, if there isn't a problem with the flash drive. Do you have an anti-virus program running that may have interfered with the file copy, or something?
In any case, BD saves are fairly compressible, so you may want to zip them as a backup rather than copy. For multiple saves something like
7-Zip's solid archive would give better compression than zip (though a little slower to create and extract saves from).
