Here’s the scenario: You remove links from pages (and templates) that point to a file you are about to delete. After careful inspection you’ve determined all of the links are gone. However, when you delete the file from within Dreamweaver a confirmation dialog appears stating that other pages are still linked to the file.
This is an internal cache issue. It seems that Dreamweaver doesn’t always update the cache to track links within a site.
At this point you could just continue and let it delete the file. However, the safest method is to simply close Dreamweaver and then re-open it. This way you’ll know if you missed any links because it will again show if there are any pages linking to the file, but this time the cache will have been updated.
I’ve seen this in happen Dreamweaver CS5 for Mac and I’m certain I’ve also seen it in previous versions, too.