My guess is you rsynced without -HS
, so that hardlinked files in the original are not hardlinked in the copy, and sparse files in the original are not sparse in the copy.
You can verify the first hypothesis doing something like
diff -u <(find /run/media/jonash/T1/ -type -f links +1) <(find /run/media/jonash/T2/ -type f -links +1)
Finding sparse files is slightly more difficult:
diff -u <(du -hsc /run/media/jonash/T1/*) <(du -hsc /run/media/jonash/T2/*)
Then see which directories show a different size, and drill down till you find files where du -h
reports a smaller size than du -h --apparent-size
.