In our case, we handled a similar requirement by keeping the applications separate instead of merging them into one Mendix project.
We have one external/portal application acting as the parent application. From there, users can navigate to different Mendix child applications using Deep Links.
The flow is:
External System
→ Parent/Portal Application (SSO login)
→ User clicks the required application
→ Deep Link redirects to Child App A / Child App B
Each child application maintains its own:
The parent application only works as an entry point/navigation layer.
If you need both applications under one deployment, then you can merge them and control visibility using roles and conditions, but for independent applications the parent + child app approach with Deep Links is cleaner and easier to maintain.
Kindly mark this as the accepted answer if it helps.