Patch for two issues.
I also have this problem with my game now. Persistent object's container object is destroyed upon re entering the layout. I even opened a previous version of my game that for sure didn't have the issue on the new stable release and the problem is there too so it's not my code messing with it.
I’ve submitted an example file for them. It looks like they are looking into it. Hopefully we see a fix soon. This all happened right as we hired a company to playtest and QA our game. Imagine if this had happened during the release month, oof. I think after the update that fixes this we may hold off on updating construct until after base release.