It’s easy: make an application (admission) wizard.

The first question should be: do you have this diploma which grants you direct admission?

If yes, congratulate them, they are done, “the admission is already in progress”; but this should be a success, not a warning. Also if they will have it soon tell them that it’s ok, they just need to wait.

If not, continue with the rest of the questions needed for admission.

UPDATE: for the flowchart part (comments are hard to edit on iPad):

You shouldn’t make them travel to the flowchart. The flowchart is the basic Information Architecture (IA) of your wizard.

What do students have? They have some knowledge of their current situation (eg. that they are undergrads). They also have a goal: they want to apply to higher ed (perhaps Masters, I don’t know). It seems they don’t have (neither they should have if they don’t already) knowledge of the admission process (also that they are automatically applied it seems).

So the flowchart should be something like:

1) are you or were you ever a graduate student of us?

If yes, go to 2), if not, go to 100)

2) did you finish your stuff yet?

2a) yes - OK, just wait. You’ll get notification soon. If not, write to dean at ouruni dot edu to make sure you are in or alternatively type in your student ID number here to query it online

2b) no - finish them first. 

100) ok, you need to have to fill out this form. Thanks.