What happens to unique buildings in occupied cities?
The Paper Maker and the Wat are transformed into a Library and a University. The other unique buildings I tried were destroyed.
I'm pretty certain that some classes of buildings are always destroyed, but there is probably also a random factor.
The XML files have some information about it, the probability of capture for the unique buildings is the following
Longhouse 66%
Bazaar 75%
Satraps Court 75%
Paper Maker 66%
Wat 66%
For the other unique buildings there is no value given, I assume that they are always destroyed.