Environment

Node version: v18.20.8
npm version: v10.8.2
Local ESLint version: v9.27.0 (Currently used)
Global ESLint version: Not found
Operating System: darwin 24.5.0

What parser are you using?

Default (Espree)

What did you do?

• Have some project
• Install latest ESLint
• Run eslint . --quiet --suppress-all on codebase
• Found eslint-suppressions.json with all counters about errors
• Remove some unused file (which have some suppressions)

What did you expect to happen?

• eslint . finished without errors with notify about left suppressions
• eslint . --prune-suppressions cleaned counters for removed file
• eslint-suppressions.json don't have counters for removed file

What actually happened?

• eslint . finished without errors without notify about suppressions
• eslint . --prune-suppressions finished without errors
• eslint-suppressions.json have counters for removed file

Link to Minimal Reproducible Example

Online IDE doesn't have terminal for generation eslint-suppressions.json and updating it

Participation

• I am willing to submit a pull request for this issue.

Additional comments

As workaround:

• Remove eslint-suppressions.json
• Run eslint . --suppress-all
• Now we see removals in eslint-suppressions.json diff