Was it the imported songs or the songs already in the project that got messed up?
Was the problem with note/curve sequence events or was it only sound events?
Import does not use the sequence/object names to determine what should be imported. You can have multiple objects with the same name. Only sound objects will not be imported if the referenced sound file name (not the sound object name) is already imported in the project. If the two projects you merged shared some sound files, then that may be the problem.