I am running into a simple issue with a resource referring to a missing parent. How would I proceed in updating the rest of the stack?

Do you mean the parent attribute of resource A is pointing at resource B, which is in code but not in your state?

The resource is in the code, but not in the provider

Which resource? The missing parent, or the child referring to it? You will probably need to temporarily break references, add aliases and maybe even edit the stack by hand. The solution depends on how it's broken.