Modify editor GUI content using mouse click

I'm trying to make a custom editor window that has a window area and an inspector-like area to the right, as follows:

It behaves as expected, but I have an issue: I need to know which window is current selected, so I'm holding the current window ID in a property, as follows:

 void windowFunc(int id){
     if ((Event.current.button == 0) && (Event.current.type == EventType.MouseDown)) {
         selectedWindow = id;
     }
     // More window stuff...
 }

and, on OnGUI function, I reset the selected window so whenever I click outside an window but inside window area, i de-select any selected window:

 void OnGUI () {
     // Some GUI stuff...
     if ((Event.current.type == EventType.MouseDown) && (Event.current.button == 0) && bounds.Contains(Event.current.mousePosition)) {
         // reset selected window
         selectedWindow = -1;
     }
     BeginWindows();
     // More GUI stuff, and a catch later...
 }
         

So far, so good. The problem lies when I need to modify the side view to show/hide content based on selected window:

 void OnGUI() {
     // The same OnGUI as before...
     if (selectedWindow != -1){
         EditorGUI.indentLevel++;
         // draw some controls over here...
         EditorGUI.indentLevel--;
     }
     // if statement is false, don't draw extra items
 }
         

This code works flawless if the amount of controls is higher than before (in the image example, if a window has more outputs than the window selected before). Otherwise, the error pops up on console:

 ArgumentException: Getting control 5's position in a group with only 5 controls when doing mouseDown

I know why the error occurs (I shouldn't change window content between a layout and a repaint event), but how can I work-around this issue? Does removing "Layout" functions should get rid of these errors (yes, I'm using Layout functions to draw the controls)?