[Jeir]

The best thing to do would be to ask your vet. But, from what I can remember...

Wet tail is generally when a hamster becomes so stressed its immune system becomes compromised and its body is unable to defend against its naturally occurring bacterial flora, allowing said bacteria to just...multiply beyond what the body can handle. It's not a new bacteria, it's just too much of it. Antibiotics will kill most of the bacteria, bringing the levels back down to something the hamster's body can handle. Antibiotics also work within, say, 5 days (don't quote me on that! Just an example!), and the remaining days are just to ensure that the bacteria doesn't multiply again while the body recovers.

Using the above, you can probably do it in stages. I would spot-clean a few days before the end of the antibiotics course (mainly just poop/pee areas, maybe food if contaminated), and then clean the toys first a day before the course is meant to end. You can also take some of the non-soiled substrate and, if you have the space, put it in the freezer to ensure the germs are gone. Give it a day or two for the scent to get back on the toys, then replace the substrate, adding in the what you took away before.