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If they get damaged in any way, the stop the advance and group up. Meaning you can keep them permanently immobilized until they flee by shooting mortar at them every 10 seconds or so. I know sapper behavior must be difficult to code but the change that was made to make them behave this way made them much less of a threat than they were before.

I think guards who protect the sapper (mining) units should behave much more aggressively and I think the entire raid should ignore mortar shells because stopping after they get shelled is pointless

I was doing an item stash or bandit camp quest and wasn't paying attention to map expiration time after I killed the hostiles. I built transport launchers and was going to use them to travel back home. I had 5 people there and I assigned 2 to be loaded with some loot. Map expired in the middle of the task and the screen for reforming the caravan popped up. Colonists that were in process of entering transport pods weren't on the list to reform the caravan, only 3 others and the entire colony got "colonist banished x2" mood debuff meaning they got automatically banished.

When a raid comes I often restrict everyone's allowed area to safe zone surrounded by walls. As per title, if the colonist has an active hunting task outside that area, he carries on despite the fact that animal is now outside. I think it may also happen with some other tasks but this is the only one I'm sure of; you might want to test different activities to see what exactly needs to be fixed.