I think leaving them off at this point is better than keeping them covered. He was probably shaking his head because they were bothering him from being covered before that.When it fell off earlier today, he was shaking his head, flopping his ears around, is that going to be ok with the bandage off? Won't he scratch and mess up the stitches?
You'd need to keep a close eye on him to see if he tries to scratch but I'd take it (the cone) off when you can watch.