You should try and find out why the router is not responding to begin with. What exactly is the maintenance that you need to do that will “impact any valid messages”?
Are you using any 3rd party products, such as archiving software which might be holding up the router? What about Domino anti-virus solutions such as TrendMicro ScanMail?
If you have a busy mail server, try using 4 mail.boxes (depending on the number of CPUs)
You can specify the number of mail.boxes in your server configuration document. We use 4 on all of our servers.
You can also try this command: tell router compact.
This will compact the mail.boxes.
The next thing you could do is to shutdown the server and rename the mail.boxes to mailold.box for example.
The server will automatically create new mail.boxes on startup.
You can then run fixup on the mailold.boxes and access them to copy and paste any valid messages from them into the good mail.boxes.