There may be pet dander/odors in your hvac.

One grumbled a bit, but the others simply moved out without incident. 

There is growing momentum/grumblings to further restrict/civically-monetize real estate in Santa Fe, especially for second homes, out of state buyers, and landlords. 

The problem is most-likely not a cat urine smell as much as it is cat dander not only on walls and floors, but inside walls, inside the furnace, any type of ducting, underneath the house if is on a raised foundation, in and on light fixtures, in window sills, inside cabinets, underneath cabinets, inside appliance, inside light switches and every place where air can move it.My company specializes in getting rid of odors that are difficult to get rid of.

We don't want to remove and replace it, though if we did we would go back with LVP.Dog odor can be terrible, but usually not too hard to get rid of.

Vinegar is excellent at odor eliminating.

When you send the tenant the itemized list of damages & costs, you may also include an item in your list that says something like: "After the tenant vacated the premises, there was a strong odor of marijuana in Rooms X, Y, Z.

Is it worth to replace floors due to pet odor? 

It needed odor removal, paint, flooring in basement, grout cleaning and painting, as well as updated lighting throughout.

It sounds like your downstairs tenant just doesn't understand what it's like to live in an apartment and should find a single-family home where there's no noise or odors from adjoining units.