I've been experiencing major issues with the App Proxy since the beginning of the month.
I'm convinced they changed something recently, and have reached out to support for more info.
This is an accepted solution.
Turns out it was a few problems, for anyone reading this if you use the shopify koa app and implement server.use to serve static files make sure you implement it before createShopifyAuth as requests to /a/proxy/manifest.json for example will attempt to re-authenticate if implemented afterwards and return a 302 redirect back to root.
Calling the wrong URL was my first problem once I sorted that out I still had the same issues, turns out that if you are calling static files in this way it will not work on a development store due to the store being password protected.