Security Deposit and subfloor

I recently moved out of my apt complex on July 23rd 2008. My landlord has
kept my entire security deposit and wants more due to damages casued by
pets.
Story:
I moved into the complex 4 yrs ago when pets were allowed by a different
Company/Landlord. The new landlord for the last 2 yrs grandfathered my pets
in. I did switch apts and signed a new lease but they still allowed me to
keep my pets (entire SD was returned from previous apt and new SD was put down) Now that I finally left the complex
they are saying that the pets detroyed the carpet and they needed to replace
the entire subfloor and I am responsible because I had the pets. Can they
change the rules like that? I don't understand why they would return my
full deposit from the previous apt and now keep all of it if I had the same
pets?

also to note: The previous tenants that lived in my apt had a dog and the
subfloor has been in place since the 70's when the building was
constructed. These tenants were not charged for the carpet but it was
completely replaced before I moved in.