These mixed itins can be a nightmare during irregular ops. A few weeks ago my US flight was cancelled so I was put into a direct AA flight. When I went to return from PHL (trying to standby early as a winter storm was setting in) I was told that because I had not been offloaded properly from my US flight the remainder of my flights were cancelled. It took an agent and a supervisor nearly 30 minutes to get my flights reinstated. Getting mileage credit is a constant sending in a form for miles. Unfortunately, until the two systems are merged successfully these bugs are probably going to continue to happen.