Having posted this in a different thread, I'm following the good advice someone gave me to post it here as well:

When you kill an NPC that is blockading one of your planets, the -60% penalty to production doesn't automatically go away. You have to actively open the planet in question in the planet tab to get the proper production rate to reset. Your planet will still produce at -60% well after you've killed the blockading NPC if you don't open the planet.

As always, thanks for a great game Dan.

The effect should still disappear automatically before your next hourly resources are added. It will not disappear 'immediately' after disabling the NPC.