Save file with script (skip warning 'modified outside Illustrator')

Hi All,

We all know that command:

app.activeDocument.save();

saves the document skipping all the dialogs and even alert that is popping out every time when you manually saving your file on a server:

My issue is that I am working on PDF files (with preserved Illustrator editing capabilities) almost all the time rather than .ai files, and everytime I use

app.activeDocument.save();

The .ai file is created.

My question is if it's possible to save PDF that you're working on same as you would manually 'Save' from the menu context, ommiting that annoying dialog about modified file?

Regards

Peter