Hey Tom,
During compaction, oak indexes wont be deleted Unless you manually delete them or remove the /:async node to trigger a reindex of asynchrounous indexes
If you are on AEM6.2, make sure you are on Oak-run tool version 1.4.8+ coz now AEM hai 2 index lanes async and fulltext async and if you run a checkpoint cleanup, it might remove both checkpoint and cause a full async index
Hope this helps.