InDesign and applescript

I've written an applescript to count the words in a document from a list of documents. Sometimes, a window opens showing there are fonts missing and sometimes it asks if I want to link missing art. I don't care about these windows and would like to close them automatically if they appear. Is there a command to close these? Otherwise, the script doesn't run automatically because of the open windows. I have to close them before it opens the next file.

Or even a command to ignore warning messages.

I appreciate any help I can get.