I think I found a bug with these missions.. and I'm hoping somebody else can confirm that this is or isn't supposed to happen before I put in a ticket. It's not a critical issue but basically what happened is I had a mission to kill 4 pirates in the Cantijaris system. I killed 3 fairly quickly when I got there. Searhing for that final pirate, I went into a USS and there was the guy there sending me a message about how they'd pay more for me to kill feds and updated my mission. I flew away and went off to find the final pirate and killed my 4th pirate in the next USS I found. Except, when I looked at my mission ... it wasn't complete... it showed one kill. Apparently when your mission gets updated with the alternative to kill feds instead of pirates, it resets your count total and you have to start the mission all over. I am unsure whether my timer also reset... I suspect it did.