The missions auto-republish, but they are not all re-published at the same time, but over time (pretty fast, actually, considering how many Foundry missions there are ). Some authors and players will continue to see more past-published missions added to the in-game search as the re-publish process continues.
Brandon "BranFlakes" Felczer | Former Community Team Lead for Perfect World Entertainment
Just to let you know, after the patch I had some weirdness on an unpublished mission. I opened it and it had a bunch of warnings about objects outside the placable area. I looked at the map in question and everything I had placed had been moved north so some of it was indeed outside the map. It was an easy fix, I just selected all of it at once and dragged it back down.
But I suggest everyone check their missions.
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