See the release notes https://world.mendix.com/display/ReleaseNotes/6.9.0 and read the section about deprecation warnings.
"Most of these cases can be fixed by making the necessary inputs be the NPEs directly so that they do not have to traverse the association. Another option is to associate the NPE with the current session (variable 'currentSession' in microflows) to prevent garbage collection in Mendix 7. System.Session is an exception on the rule, traversal from System.Session → NPE is allowed. A more detailed guide will be available with the Mendix 7 release."
Although these associations exist on many projects, I have never traversed the PE -> NPE path in my projects (it seems the associations remain, but the traversal has become one way), so the problem may not be as big as you assume it is.