You can read the .mlt XML, which records in time clock values, which is slightly different than what appears in the UI, which is a time code. Still, the UI does accept when you paste the time clock value into somewhere like the timecode display below the player. But the easiest thing for you to do is simply change the file names of the video files to make the project refer to the file you want.
If you do not want to change their names simply do something to break the project file’s video file name references. You can move either the project file or the O-video file from its original position. Then, when you open the project, Shotcut shows a Missing Files dialog. From there, you pick the replacement file.