I'm not sure off the top of my head, but did you check to see if reloading triggers an ApplicationMgr.DisplaySequenceFileEvent?
If not, you might be able to post a deferred call from ApplicationMgr.QueryReloadSequenceFile (.net Control.BeginInvoke is one option), but you would need to not return QueryReloadSequenceFile_Prompt from the event because that would trigger a dialog box whose event processing would allow the deferred call to execute before the user can choose whether to reload.