ATM, when you clone a category all articles inside that category are clone "as is", including cross-references between the articles.
This yields the following issue. Imagine the simplest case where you have a category (catA) with two topics, e.g. topicA1 and topicA2, and topicA1 has a cross-reference to topicA2. Then you clone catA to catB. If you now click the cross-reference in the cloned topicA1 (or topicB1), you will open the original topicA2. Actually, I would expect that the cross-reference is updated and links to the cloned topicA2 (or topicB2 if you like). At least, I'd like to have an option to determine the behavior.