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But in general I don't think it's strictly necessary unless your turret line was struggling to keep off the attacks. In such a case you could just wait until the red ammo is used up. In the "hotspots" at your wall you will soon see green ammo being used. In other areas there no natives pop up the turrets might keep their red ammo for a long time, but this shouldn't be a real problem.
You can use a deconstruction planner to pick up just the turrets and then a blue print to put the turrets right back.
If you have an exoskeleton or 2 in your power armor it will be faster to run along the row of turrets and hold CTRL and left mouse. You will have to run back along the turret row a second time to take out the ammo that was in the inseters hands to clean all the red ammo out.
If it's an 'active line' you may need to play several filter inserters so just incase if the line gets for whatever reason, gets the ammo mixed you will still be filtering out ammo. If some parts get pure.
At hundreds turrents it may take awhile but it's automated and large bases are more like a living thing with medication it takes a while for tiny changes to take a large effect. It sounds like you're getting there so I would wait, 5, 10, 30 minutes to an hour before looking for "real" results.