fix: clean stale checkpoints

[luke-lombardi]

Summary by cubic

Cleans up stale checkpoint state to prevent stuck restores. Deletes orphaned sync files when checkpoint data is missing and waits for both the sync file and data before continuing.

• Bug Fixes
  • Remove sync file if checkpoint data is missing to force a fresh S3 re-sync.
  • Wait for both the sync file and checkpoint data before proceeding.

^{Written for commit ad996d8. Summary will update on new commits.}