I doubt clearing Tomcat instances or I*E compiled tasks will help at all here (most especially the former as there's no JSP involved here).
The underlying issue is clearly: wt.fc.ObjectNoLongerExistsException: "wt.doc.WTDocument>9205053...
So you're trying to operate on a document that no longer exists at this point. If so, then, yes, you'll tend to get a good deal of exceptions about that.