I have the same problem. Here is a generic recipe to reproduce, assuming a repository X with a submodule Y (set with an `https` URL):
1. `git clone ... X`
2. `cd X`
3. `git submodule sync`
4. `git submodule update --init --recursive`
5. `git remote rename origin remotex` # rename the remote in X, not Y
6. Elsewhere, add a new commit to Y and create a branch "update-y" in X, pointing the submodule to that commit. Suppose the hash of the new commit in Y is `abc1abc`.
7. `git fetch remotex`
8. `git checkout update-y`
9. `git submodule sync`
10. `GIT_TRACE=1 git submodule update --init --recursive`
- observe:
* the command in the last trace message to be `git fetch remotex abc1abc` (should be `git fetch origin abc1abc`, because that is still the name of the submodule's remote)
* the wrong error message complaining about 'file' protocol (which isn't involved anywhere)
