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If you have coordinator kill enabled

druid.coordinator.kill.on=true

(see https://druid.apache.org/docs/latest/configuration/index.html#coordinator-operation) then segments will be permanently deleted them from metadata store and deep storage when marked unused If you leave this setting to false, then unused segments will be retained in the metadata and deep storage but not loaded onto historical nodes

is there any way of querying metadata store for the unused segments via druid sql? it seems when I mark segments as unused they are gone from sys.segments table

The unused segments are still there. If you do not run a kill task on the datasource, segments will still show up in the metadata database, not the sys.segments from the console which is filtering them out, but rather the druid_segments table in the metadata database which shows it with

used=false

.

the unused segments do indeed disappear from the sys.segments table (that table is for segments that are active or recently been active) for performance reasons. What is your use case for querying their metadata? Is it just to check that they are indeed there?