Re-organizing main blogs upload folder

After several years of using wordpress multi site I find myself in a predicament.

I see that the main blog is not using the year month organization for the uploads folder. Is there an easy way to modify it so that it will effect the image currently in the uploads folder?

I know I can change it for future uploads, but would really like to migrate everything to that new system.

Reason for doing this is I have approx 96,000 uploads with a size of 7GB and am finding it difficult to backup.