I’ve never done WL/Oxine (which is much cheaper and just as effective IME, you get a ton of it: https://www.healthyhoof.com/articles/Thrush/ThrushRevisited.html Scroll about halfway down the page for instructions) with glue ons on. I’m not sure if it would harm the glue bond–I would think it might, but I suppose there’s only one way to find out. Though if my choices are between having to re-glue a bit early or letting WLD fester, I’d probably take my chances and just give it a shot.
If I pull shoes off a horse and find funk, or want to glue but am concerned about funkiness, I’ll keep them in boots for a few days first and do a daily ~30 min Oxine soak. For really bad ones I’ll do 3 or 4 soaks, for ones that are just a bit gross I’ll do 1 or 2. I try not to glue until 24hrs after the last soak because I don’t want it to affect the glue bond. It’s possible that’s just superstition, I’m honestly not sure.
Then when I go to glue, I do a quick pass of a torch and I smear as much Artimud or medicated hoof wax as possible in any funky spots. You can roll a ball of product into a noodle type shape and then shove it into the white line using a finger or a hoof pick. I’ve had good luck clearing it up this way.
Did you apply any antifungal/antibacterial product underneath the glue ons?