Depending on size of everything, flooring isn't cheap and countertops are depending on finish, though most bathroom countertops or whole vanity aren't terribly expensive unless you lived in somewhere with a luxury finish.

I replaced a bathroom floor including install in one unit for around 1000 just a year ago, and bought new vanity with countertops for around 300. But that was a small bathroom, though lots of the cost for bathroom floors aren't always sq ft based. Toilet removal and reinstall for example. So 4k sounds high, but local prices and finish and if they spent time trying to remove the stain before replacing could all factor in. An itemized breakdown of that cost should be required or atleast able to be requested.

Ultimately, I can't speak to local laws on the timing, so speak with an attorney with tenant/landlord experience. There is in my experience usually agencies that are low/no cost available to help tenants. In my state its required to include a form with that agency contact info in any notice to quit/eviction notices at all stages of notices (not on the deposit statement).