Is there a way to make the process run through Application servers faster?
Yes, there is! By default, if you choose to have Reader/Author fields changed in a database, all documents are checked to see if any such fields exist. You can create a hidden view in databases that preselects these documents. Simply name the view ($adminp). The Lotus Domino Designer Help provides documentation on creating this view. There is also a ($adminp) view in the Personal Address Book (names.nsf) on your workstation if you would like to see such a view in action.