Verify latest release

• I verified that the issue exists in the latest pnpm release

pnpm version

No response

Which area(s) of pnpm are affected? (leave empty if unsure)

CLI

Link to the code that reproduces this issue or a replay of the bug

https://github.com/abejfehr/pnpm-skip-build-issue-repro

Reproduction steps

1. Create a new project with a pnpm-workspace.yaml file with strictDepBuilds: true
2. Run pnpm add sqlite3, and observe that this fails because an ignored build
3. Add 'sqlite3': false to the pnpm-workspace.yaml file under allowBuilds
4. Run pnpm install, observe that it still fails for the same reason
5. Run rm node_modules/.modules.yaml
6. Run pnpm install and everything is fine now

Describe the Bug

It feels like skipping a build in pnpm-workspace.yaml doesn't invalidate the cache.

If you allow the build with true, then it does.

Expected Behavior

I would expect to have been able to run pnpm install without failure after adding 'sqlite3': false to my allowBuilds

Which Node.js version are you using?

25.5.0

Which operating systems have you used?

• macOS
• Windows
• Linux

If your OS is a Linux based, which one it is? (Include the version if relevant)

No response