You can try to rsync the files again by using rsync tool:
$ rsync -autN /source/* /destination
or (if there are too many files):
$ find /source/ -name \* -type f -exec rsync -atN {} /destination/ ";"
Here are the arguments:
-a, --archive archive mode; equals -rlptgoD (no -H,-A,-X)
-u, --update skip files that are newer on the receiver
-t, --times preserve modification times
-N, --crtimes preserve create times (newness)
If this won't help, try without -u.