fix(file source): fix checkpoint write race on shutdown and flaky tests (#25447)

* fix(file source): fix checkpoint write race on shutdown and flaky tests

* fix clippy: use Arc::clone instead of .clone() on ref-counted pointer

* refactor(tests): rename wait_for_atomic_usize_timeout to wait_for_atomic_usize_timeout_ms

* changelog: file source checkpoint write race fix

* Format

* Remove data loss from changelog