given "1st moodledata, the storage is 3gb and 2nd moodledata the storage is 6gb".
Thus, keeping in mind what Davo said, one would 'cp' 1st moodledata into 2nd moodledata which hopefully would result in fewer orphaned files? (if am thinking correctly)
To address orphaned files, install moosh. There are a couple of moosh commands that deal with status/state of filedir/mdl_flies table and orphaned files.