I was able to resolve this issue by navigating to the Xcode Cloud Settings in AppStoreConnect and manually re-granting permission for the repo connected through Github. You can do this through Xcode by going to Product -> Xcode Cloud -> <Your App> -> Manage Repositories.
Make sure that you are also signed into the account you originally setup Xcode Could with. There should be a button next to the repositories connected that says grant . Clicking this should hopefully resolve your issue.