In this new version 25 each tab of 2d or 3d window can either show same or different layer on off status. Just go through tab settings help in AC help and you will understand how easy it is to control on layer display in each tab.
each view uses it's own stored layer combo (which can technically be "custom"). To ensure that an element is visible on a set layer combination, make sure you are clicking the "update" button near the bottom left after making the layer visible in the right hand column of the layer combo dialog. You can also select a layer in the right hand column, and make it visible for each layer combo in the left hand column, and avoid the "update" step. Last thing to make sure is that the various elevation/plan/3d/section/etc views in the view map are using the correct layer combo. If you are navigating primarily with the project map instead of the view map, then layer combos are going to revert to the last layer settings used for that viewpoint type. here's a video I did a while back on quickly updating groups of layers: https://wwabim.wordpress.com/2020/04/10/layer-adjustments-in-Archicad/
BIM solutions and trouble shooting (self proclaimed) expert