A resolution to this issue hasn't been found, as tech support weren't able to recreate the scenario. The problem appears randomly.
A second project had the issue of sections set to show new & existing elements, the wall linings (not the whole wall) were being intersected by the demolished building that was hidden. No view settings were changed.
This was able to be worked around by isolating layers, but the problem was still the same - the saved view & view on layout were changing on their own.
ArchiCAD 18/Windows 7/16GB Memory/i5 3.2GHz Processor/NVIDIA GeForce GT 610