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It depends how you want to change the axes. You can rotate them as a whole, but you can't change them relative to each other. For example, you can't reverse the direction of the x-axis without also reversing y or z, which would constitute a 180° rotation. This is because, as stated in REP 103, all coordinate systems are right-handed, and reversing only one axis would make it left-handed.
If you want to rotate the whole frame, use the rpy attribute in the elements you want to rotate. Have you looked through the URDF tutorials? The Building a Visual Robot Model with URDF from Scratch tutorial involves rotating links.
If I missed the point of your question, please clarify what you would like to know.
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