Cherryrock --- Have you tried doing it on sewing machine bobbin winder? With a little care not to tangle it just might be possible. But, the expense of all those bobbins might be a bit costly.
I was in same fix. Or very similar. Filled 5 tightly packed thread boxes crammed full. Had to hand wind all with that DMC hand winder. It took a few days doing practically nothing else. But, got the job done. Glad I took the time. It sure made stitching a lot more enjoyable. No more searching & comming up empty handed looking for a specific color #.
Once you set your mind to doing it & sticking to it till the job is finished you'll be glad you did it , too. ----- Citrine1