Did you solve all your other problems as well?
The disappearing furniture are because they are either not visible because their Layer is hidden (set in the Layer Combination that is part of the saved View used by the Drawing placed on the Layout) or your Library containing those Objects is not linked to the Project.
The Walls are transparent because of Model View Options settings, namely the Override Cut Fill Setting in the Model View Options Dialog. This is another setting that is stored in saved Views.
About the Window Markers: select all Windows and in the Window Settings Dialog go to the Dimension Marker panel. This is where you can set the size of your Marker, its Geometry, Marker Text, etc.
Yes,it is possible for many settings to transfer them from one Project to another. In case of elements (in our case, Windows), you can copy-paste from one Project to another, then acquire their settings and apply to other elements. So go to the "Normal" file, select the Wall with the Window in it, press CTRL+C to copy it to the Clipboard, switch to the "Ruined" file, press CTRL+V to paste it to that file. Then ALT-click the Window to acquire its settings, and CTRL+ALT+click on other Windows to inject these settings into them.
Pen Sets are attributes. Attributes can be exported to/imported from other ArchiCAD files in the Attribute Manager Dialog.
Model View Options can also be transferred because in the Model View Options Dialog you can export them to an XML file and import that XML file into another Project.
(If something is not clear, please look them up in the Help files for more detail)
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