Qualpo do you know if theres a way to get all currently loaded resources
I don't think there is. Resources are memory managed via regular refence counting mechanism that's used for all other ref counted objects. You'll have to write your own bookkeeping system.
If everything in your pack file has its known place and you always load all of it, then simply do it via filenames. Reload all files using the replacement flag. This should refresh the data in every existing object associated with a specific path without re-creating the resource object itself. So all existing references will still be valid, and have access to newly replaced data. Haven't tested it though.