I have seen and heard of accidents in URD transformers with different phases in it. Unfortunately, none of the accidents were related to the fact there were different phases in the transformer...... They were all caused by someone doing something STUPID!!!
By itself, having different phases in a transformer, is not dangerous. If you, as a qualified lineman, do what you are supposed to do, it will not present a danger to you.
If it happens, make sure the mapping is updated to reflect the change, and make sure the cables are properly labeled.
KEEP WORKING SAFE!!!