You should keep a close eye, since he’s not showing any signs nof illness, he’s eating, pooping and playing it doesn’t sound like an emergency.
Clear discharge is not as indicative of bacteria as thick, white or yellowish discharge, but when there are bacteria, a week is often not long enough to eradicate them. Did you see any improvement at all from the abs when he was on them? If you did it could mean some of the bacteria were killed off but some remained and started multiplying as soon as the course of abs was over.
I’m assuming your vet didn’t do a culture. It’s often not done because if the standard antribiotic fixes the problem, that also diagnoses the problem. But if the problem persists or gets worse, you should look into it further. Some bunnies are actually allergic to some types of hay. A young bunny’s immune system is not fully developed, same as with small children. Healthy food is key, good quality pellets, grassy hay of good quality, perhaps alfalfa hay, and now at 12 weeks, you can start introducing fresh leafy greens, one at a time, a small piece only, with a close eye on fecal output.