I was working in one collection/layer, and noticed a few of my objects were not showing. After looking, the vast majority of my objects are currently hidden/missing. They are not hidden like I am used to (h/alt-h). Link to file is down below since BA cant accept it
When I opened your file and let it load your UI settings, there was a lot missing. However opening your file and not loading the UI gives me everything. You could try to do it that way. Not sure if there was some sort of visibility thing to cause it to be save with the UI this way or not.