Afraid no help can be given ... the DB you imported has newer information/meta data that what's in the older moodledata/filedir and other directories - just like menu says ... orphaned - there's data in the DB but no files/resources etc. that match in moodledata.
A minimal clone of production site would need to include at least the moodledata/filedir directory and I'll bet that's the lions share (largest) of what's in moodledata.
Depending upon operating system, one could see how large filedir really is:
cd /path/to/moodledata/
du -h ./filedir/
That probably will take a long time to execute and probably hefty on resources of server so do that a non-prime time for users.
'spirit of sharing', Ken