Comment 1 for bug 1843894

When you say some jobs are using the snap, do you mean using the applications exposed from the snap in $SNAP/bin?

While it's unclear exactly what is not atomic here, it sounds like this might be fixed somewhat by using refresh awareness, but it's not clear to me if the snap is actually being refreshed or not. See https://forum.snapcraft.io/t/wip-refresh-app-awareness/10736 for details of how to try this out and see if it fixes anything for you.