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This is not cristal clear
I suggest you add screenshots to explain better:
we also migrated our environment from 2009 SP5 to HOPEX V1R3 last month and were surprized about missing Messages on diagrams.
You could configure the settings to display the messages as follow:
MEGA-Administration Tool -> choose environment -> options -> modelling processes and architecture -> usage of messages on diagrams
The screenshot is not displayed.
Please open a case with MEGA Technical Support. This will be easier to gather symptoms
Note also that the diagram 'application environment diagram' is disabled by default with HOPEX V1R3
It can be restored with a compatibility option
It is still enabled by default with HOPEX V1R2