Hi @kanlukasz
There are situations where you can clean up some data… and others where it may be prove to be more difficult.
Here are a few threads offering possible solutions. The last thread discusses this topic/concern in great length… offers workarounds… etc. All links below are worth a peek and can potentially help you on a case by case basis. Hope you get this resolved!
Removing data from WP db after deleting a field group
Deleting field data manually from DB
Flush Unused Custom Fields
