Simon made it both to Ireland and back even with his expired Swedish residence permit. We did end up having a tiny drama leaving Sweden when it was discovered Simon had overstayed his visa here. At least on paper, once the application for an extension is in the permit is extended until a decision is made but since our application hasn’t been processed yet it doesn’t show up in the systems.
In the end the police at the passport check let Simon travel when we explained that we’ve handed in an application for an extension and that we’ve been told that travelling was ok once the application was in (which was what Simon was to when he called up the Migration Board). We had the document from the Migration Board (confirming that the application was registered and the date for that) with us which I think helped.
In the UK, where we transferred flights, and Dublin there was no drama. Entering Sweden again (which we thought might be an issue) went smoothly too. So in the end we were nervous for nothing.