Sorry, not a minimal reproduction, but running this in the rust-analyzer repo seems to reproduce it:
$ git branch test-merge 4bf516ee5a960c1e2eee9fedd9b1c9e976a19c86 # last commit before smol_str
$ git checkout --orphan empty
$ git rm -rf .
$ touch xyzzy
$ git add -A xyzzy
$ git ci -am "First"
$ git switch test-merge
$ git merge --allow-unrelated-histories empty
$ rustc-josh-sync push [...]
[...]
Josh created a non-roundtrip push! Do NOT merge this into rustc!
Expected 6d7e78d196a4b8482d8537283d2b04dddc1e4fbc, got 7ff61f7cdd2b10c2bcf3379911180cb8a9e3ca9a.
See rust-lang/rust-analyzer#21008 for context.