How to repair a store after manual changes with hardlinks-global?

[donferi]

How can I repair the store after modifying it?

Some context: I'm using the following .yarnrc.yml in two projects, project A and project B, on macOS.

Running yarn 3.3.1

nodeLinker: node-modules
compressionLevel: 0
enableGlobalCache: true
nmMode: hardlinks-global

If I install let's say is-even in project A and project B, they are hard-linked as expected. If I then I go to project A and modify node_modules/is-even/package.json I can go to project B and see the changes there too.

My question is, how can I restore this modification? I tried yarn install, yarn install --check-cache, yarn install --immutable but nothing errors out or reverts the change. The only thing that worked for me was to rm -rf node_modules in either project and run yarn install again, but this seems like not the right way to go about it. What am I missing?