If leaving her ears alone for a couple of days still results in the same redness, flaking, head shaking, irritation, I'd be highly suspect of mites, esp. after the visible bugs you mentioned.
After reading the thread, I can't help but wonder if the vet did not use a scope to look in the ear, how can they be certain? My apology if I missed something that stated the vet confirmed it was not mites. Mites cause dry skin, scaling, flaky, inflamation, shaking head - what you're describing. They and the larvae burrow in hay and other bedding. Since you have an indoor bun, it might be that the hay arrived with an infestation - those tiny bugs you can see and possibly the mites you can't. Left untreated, if the issue is mites, it can lead to inner ear infection, requiring additional medicine/antibiotic. To be safe, I'd pursue as if it was after finding the visible bugs you have. Consider new hay from a different source (online store, prepackaged perhaps - at least until this is resolved?). This site has some useful info.
Do rabbits get ear mites? - Vet Help Direct From the site:
"During the course of treatment, all bedding and food must be disposed of and fresh provided daily. Shredded paper bedding may be used as it is easy to destroy and renew each day. Hutches, brushes, toys, food bowls and drinkers should be disinfected daily and thoroughly rinsed so that the rabbit is not affected by the cleaning agent. Wash any blankets or fabric toys at 60 degrees. In this way any mites or eggs will be destroyed so the rabbit cannot be re-infected. Mites can survive off the rabbit for 21 days so keep these measures in place for a month."
I've also read a home remedy is 6-7 drops of olive oil using a dropper can kill mites by drowning them but check this with someone more experienced. That said, if this issue is mites, you'll need to follow the steps to get rid of the larvae to truly eliminate. Best wishes!