The Exchange Utility is not reconstructing stub messages using the ESM service account which is running as a local administrator, upgraded recently to AM 5.3. From the EU logs you can see that the process starts but suddenly stops with no errors or warnings as follows:
Event Viewer Error:
2020-09-29 15:39:58,147 [49] ERROR EU.URLRepairThread - {{c86972a2-df3e-43fe-9df3-061620e71ba2}} Error while updating URL 'https://am.cityofithaca.org' for messages in MailBox 'Dan Cogan'
System.ComponentModel.Win32Exception (0x80004005): Unknown error (0x8004011d)
at Quest.AM.MAPI.MAPIUtilityV2.IntermediateObjects.Row.IMSession.OpenStore(ENTRYID storeID, IntPtr uiParam, FLAGS openMsgStoreFlags)
at Quest.AM.MAPI.MAPIUtilityV2.PublicObjects.Items.Session.OpenStore(ENTRYID entryID)
at Quest.AM.MAPI.MAPIUtilityV2.PublicObjects.Items.Store.Open()
at Quest.AM.Tools.ExchangeUtilities.Threads_V3.ThreadBase.OpenStore(Session session, ProfileInfo delegateAccountInfo)
at Quest.AM.Tools.ExchangeUtilities.Threads_V3.Threads.URLRepairThread.Start(Object o)