When you reactivate the completed manhunt it doesn't reset the overall progress for the prime target it allows you replay the hunt to get the bounty again for example rehunt venus or neptune etc etc .Also if you check the manhunt tab it will show the percentage to find the prime target, like when neptune was up and killed it showed 25% for jupiter now it will be 50% after hunting the new target etc etc so no need to worry.
Same thing just happened to me, and it DOES reset your progress, I was at the final bounty for Venus, the bounty wasn't showing up anywhere for some reason and so I clicked "reactivate manhunt" thinking it was toggled off like some of the other event things like polarity... nope all my progress from the last few days wiped, literally just completed DARPA and it's all gone...