Wow! 6000 sites! or do you mean courses? ;)
If I'm understanding correctly, there is no 'internal' to Moodle 2 'easy button' for doing what you desire (at least have not found any ... yet). [unless one is a guru with MySQL]
Have found that almost any direction one takes to avoid legacy requires labor ... on the server end and teachers as well - and each has to do their part.
This may not work in your situation, but it's 'something' ...
If you still have the 1.9 data directory, one could create a file respository in the 2 called 'olddocs' and copy the cleaned up course ID folders from the 1.9 data directory to the new repository. By 'cleaned up' meaning delete the backups and backup directory in each course ID folder and delete the moddata folder. That could be accomplished by a rm -fR command. Copy all but the '1' folder ... that was for the front page of the 1.9 site.
You'd have to gen a report/print out of what course ID belonged to what course/teacher for the next step.
In the 2, at the course level, one could then create a file system repo that points to 'olddocs/[courseIDfolder]' per teachers course. If they had multiple course, then mulitple repo links.
Teachers could then re-link files in their course to those repos. Once having done so those files/links become part of the new document management/filing system and backups should loose 'legacy'.
May not work for you. But, hopefully, it might 'spin' another idea. ;)
'spirit of sharing', Ken