I had been playing using a number of custom gangs for a bit and had managed to accumulate about 74 infamy points.
I decided I'd resume the story (I had gotten to story mission 3 previously). I started the mission and quit shortly after launching the mission. When I returned to my custom gangs found that all infamy points previously gained had been lost and I was back at 0 points.
One of my custom gangs shows as having -74 Infamy on the Infamy screen now.
From what I can tell, in launching (and quitting) the story mission after having played a custom gang has completely reset my infamy points.
Is there any way to get back the previously lost infamy?