I'm working on an InDesign document that makes extensive use of linked Illustrator graphics. Many of these Illustrator graphics themselves make use of placed png images.
The problem I've run into is that if I update a png for one of the Illustrator graphics, InDesign doesn't pick up the associated change (because the .ai file doesn't think it has changed either). The only way to get the updates to cascade through is to open the .ai file, make and undo a trivial change, and then save.
Is there a way that I can tell InDesign to thoroughly update all links, regardless of whether the file stamp says a file has changed or not?
From what I understand, you are saying that your files aren't updating after you make changes to them in Illustrator.
Try this; Go to your links panel (if you don't see it then select it under your "Window" tab). There you should see all of your files in your InDesign document. You can look through all of them to find the file(s) in question, or you can sort through them with the little tabs.
When a file changes outside of InDesign, it won't always update, but the link file in the links panel should detect the change. It will have a little caution triangle by the file name if the file has changed. Double click on the triangle and your Illustrator file should update.