Is is really worth it to take the LL to court over such a small amount. If I were the LL, I too could come up with a letter saying that this was not preexisting.
BTW, I doubt they can determine if it was preexisting dating back to the time you first started your lease. But, for your money they would be more than willing to work with you on that.
I'm assuming that it'll be more than just a standard cleaning fee(they'd pull up carpet, give us a day to remove the padding, and put down new(if its needed), possibly seal the floor if it got down that deep, clean the carpet top and backing, use thier anti odor stuff on it, extract again, then put carpet down again) Thats not even including the price of carpet padding, my time, or the possible sealant.
They said the amount of crystalization of urine should help give them an approximate timeline of how long ago this happened (especially if the cat urninated in the same place over and over again). Also if there are older stains in the floor boards they would be able to tell if they are recent or older, depending on how far rotted they are from the bacteria that the urine produces. They are willing to do this evaluation for free, so no money on my part to have it done.