cargo upgrade fails when replacing crates-io with another registry

Hello, I am not using crates-io, my `config.toml` looks like this:

```
[registries]
my-registry = { index = "sparse+https://" }

[source.crates-io]
replace-with = "my-registry"
```

I can build fine with `cargo build`, `cargo update` works fine to update my `Cargo.lock` file, but running `cargo upgrade -v` is failing with this error:

`Error: The repo at path ....\.cargo\registry\index\ is unusable due to having an invalid HEAD reference: reference 'refs/heads/master' not found; class=Reference (4); code=NotFound (-3)`

Any ideas on what I could do to get past this problem?

Start by reproducing `cargo upgrade -v` with the shown `config.toml` and replacement registry, then compare its registry handling with the successful `cargo build` and `cargo update` commands. Done means dependency upgrades work without the invalid HEAD reference error when crates.io is replaced.

Written by the indexing model from the issue text.