by Jon Fila.
Okay, it looks like this was part of MDL-28019. Here's how I'm dealing with it in the meantime in case anyone has the same problem:
In Chrome click on Settings: Under Privacy click on Content Settings. From there you can disable Javascript. Then go to Moodle site and click on edit settings in any of your resources that are still linking to "deleted" files. Under the content area you will see all of the files still being linked to. You can delete individual files there and save.
