Changing your theme is something that you will probably do at some stage during your stores lifecycle on Shopify.
How can I prepare Shogun for a theme change?
The good news? You don't need to do a thing. Shogun will automatically install when it needs to run on the new theme when it runs.
If you do notice any issues with your pages, simply republish the pages and this should resolve any other issues that you may have.
Please note that Shogun does not currently work on unpublished themes, however, we do have an article detailing some more details on workarounds for this,