I've also charged the tenant for the cost of professional cleaning and odor removal, but then applied the money towards replacement flooring costs.

Dead animal odor will typically go away after a couple of weeks.

Cats are quiet, but the odor can impact the neighbors and destroy an apartment if the Tenant doesn't take care of them properly.If you allow them, what do you do to mitigate your risk?

Must have been more odor in the nooks and crannies of the windows (with those pane bar things) than I realized.  

If you had chosen to just flip the Contract to someone else "as is" (no repairs) for no other profit margin, you still would have kept that $200K that would have been spent on renovations, no fuss, no foul, it's your money.In month 14 after you have spent a lot of time and $200K on repairs, the owner gets drunk and plows his car into someone else and is found liable for killing someone. $2 million judgment against him. 

The odor is back !   

Sounds like, aside from the odor issue, they've been paying on time and haven't really given you any issues as an inherited tenant until now.

Kilz also makes a low-odor version, works almost as well as the regular stuff.

Even if they swear they'll never smoke inside, they will, and will drive your other tenants nuts and it's expensive to get the odor out.Get your tenants to pay online so you aren't chasing the rent check.Be direct with tenants. 

It look like a home run but it was a foul ball.