If you are using Application.cfc, you can update it so that you can force a call to onApplicationStart() if something specific is passed in the url, or something similar. Simply place a check for that magic token in onRequestStart(), and call onApplicationStart() if it is.
If you are not, you can try @Marcos's suggestion. I'm not sure what ramifications that may have in your application. What I would suggest is actually renaming your application, so it starts as a new app.
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