Bypassing legacy save dialog in script...

  I have quite a few scripts which work on batches files.  One problem I consistently run into after upgrading AI is that there's the dialog that comes up for each file as it's saved warning about writing to a legacy format.  Now, I know I can check the "do not display this again" checkbox and be rid of the dialog, but I actually want to keep that dialog for when I'm manually working on a legacy document to remind me that it is a legacy document.

   I'm looking for a way to either A) bypass the dialog and continue saving in legacy format, or B) save in the latest AI format.  One thing I've tried to do is use document.saveAs() instead of document.save().  However, that introduced an issue where AI will not overwrite the file because it's open. Wondering if anyone has any ideas.

Thank you!