If we found a way to take a phonecall during a mission we would be set. That would require being able to take a mission while holding Tab while doing your trick. Any ideas how to do that? I am gonna test that as well tomorrow I think.
One thing that I have not tried is the following (you have probably heard this one already):
Maybe CJ got a phonecall from Denise (because of the lack of dates with her) the exact same time he entered the mission marker. This prevented the flag from getting set to 1 OR it reset the flag to 0 after the call was over. This would explain the progress loss after the mission start.
I am curious about one thing before grinding this theory: What is the delay between the time the Denise phonecall ends and the time the progress drops? We have to test this, if our testing time corresponds to the 'evidence' VODs, we might be on to something. If it does not, it is not worth testing this theory.
Other idea: test taking phonecalls as you enter the mission marker. Other idea#2: test taking DELAYED phonecalls as you enter the mission marker. Other idea#3: test taking TIMED (might not be the best was to phrase it) phonecalls as you enter the mission marker. Eg: Low Rider race.
http://pastebin.com/jt510MJ5 This pastebin contains the conclusion of my testing of mission duping in SA. The glitch is still yet to be found, though, I wrote down some of my ideas in the pastebin.