I think what you need to do is to freeze your map scale and Layers in order to avoid being adjusted or modified if you did any zoom in or out in the map canvas. I am not sure if you did the following steps or not, but you can freeze you maps as follows:
(1) In the map freeze the scale by clicking on Expression as you can see below
(2) A new Expression window will open, then you enter the desired scale, ex 500000
(3) Then check the boxes of both 'Lock layers for map item' and 'Lock layer styles for map item'
Following the above steps, you will freeze your layout based on the desired scale and layers mapped in the canvas. When you need to update your layout based on any changes in the map canvas, you can just uncheck the the boxes of step (3) and click on refresh, then re-check the boxes again.