Just to get an understanding of what is happening here.
"using Surveyor in Session Mode"? - I assume means that you have loaded a Session to edit while in Surveyor.
"changed the layer to root or any other" - I assume means that you opened the Layers tool and selected the root layer (Route "root" layer - the top layer in the Route Layers group
or Session "root" layer - the top layer in the Route Layers group? Confusing, I know)
You then made scenery and/or rolling stock changes to your Route/Session, went into Quickdrive, ran the trains and then exited Quickdrive and returned to Surveyor.
On opening up the Layers tool in Surveyor you noticed that "layer level" was as you left it. By this I assume that the layer you previously selected before entering Quickdrive was highlighted ("selected"). The highlighted layer is referred to as the
Active Layer, it is where assets will be placed when added to the Route or Session.
On returning to session, the layer level was as I had left it. e.g pointing to root or wherever. Now whichever layer one had before Quickdrive is overridden and it always reverts to session layer.
I do not understand this. The second sentence seems to contradict the first.
Since Trainz Plus does not have QuickDrive (it has the Unified Driver Surveyor interface instead) I cannot try it but I suspect that you may be referring to an old problem that has existed since T:ANE (and possibly TS12) where Trainz loses track of which is the active layer when saving routes/sessions. If so then it is not a new "feature", "bug" or a "mistake" but just an old problem.
The issue of not knowing which is the active layer, and therefore which layer will receive newly added assets, is also an old one and much complained about. Fortunately, according to N3V, it will be fixed in the new Surveyor 2.0 that is coming real soon(TM).
My thoughts.
EDIT: In the meanwhile, there is a Trainz Wiki page that gives a detailed description on using layers where you might find a few "sanity" tips - such as locking layers. See
https://online.ts2009.com/mediaWiki/index.php/How_to_Use_Layers