cargo sqlx prepare only works after cargo clean

[FrenchGithubUser]

I have found these related issues/pull requests

https://github.com/launchbadge/sqlx/issues/788

Description

cargo sqlx prepare removes some files (without adding the same amount) in .sqlx/ when changing a query in the codebase. cargo clean does fix the issue, but it seems like running cargo sqlx prepare multiple times ends up producing the correct output as well.

Reproduction steps

cargo sqlx prepare

SQLx version

0.8.6

Enabled SQLx features

"runtime-tokio", "postgres", "chrono", "ipnetwork", "json"

Database server and version

Postgres

Operating system

asahi linux

Rust version

rustc 1.89.0 (29483883e 2025-08-04)

[abonander]

@FrenchGithubUser can you please provide an example project that reproduces the issue? Otherwise there's no place to start here.

[FrenchGithubUser]

https://github.com/Arcadia-Solutions/arcadia

Run sqlx prepapre in backend/storage, then edit one if the queries there, and re-run it

[FrenchGithubUser]

Those are the files that are making the schema-check fail when missing (in .sqlx):

https://github.com/Arcadia-Solutions/arcadia/commit/af9eceb83893ceba780ecf538afb2fab8e140e9e

I removed some old code thinking it might be the issue, but that didn't help.

Also, running cargo sqlx prepare --check locally works fine