Linking Model to Viewport

I just had an interesting “go around” with my Layout program regarding scene updates and reference update. First, I have a small cottage that has a deck on the side. I created all my scenes and inserted into Layout and everything has work fine. That is until I deleted the deck. I updated all the scenes that showed the deck in SU and that worked fine. I went into LO and updated my reference and the deck disappeared from four viewports and remained in the fifth. I could not get the deck to go away by doing scene updates several times and reference updates. Then I happened to activate the viewport and look at the model tray and I discovered that not all my scenes were listed. That indicated that I was not looking into the proper model - don’t know how two references models were there. Anyway, I relinked the proper model and bingo, the deck went away and all is right with my Layout presentation. My question is: how did the viewport become unlinked from the reference model and why did I not notice it? In the reference box, I see that along with the model, there is an embedded file by the same name. Could the viewport have been linked to that embedded file and not the proper one? What can I do to make sure that it does not happen again?

I just noticed that after my relinking of the model to the viewport, the embedded file has disappeared.