Hi,
I use MySQL as datasource.
When I delete a precious stone (for example City Protecion) in game the block is deleted but the protecion remain (I see it with the diamond picaxe) and I must do /ps clean to resolve it, can you avoid this problem?
Regards.

Are you using worldedit's superpickaxe to break them?

yes :/

Yes superpickaxe changes the type to air rather than breaking the block. So there is no fix for this, you must break a pstone to remove it rather than change its type. To remove orphaned pstones from the database use /ps clean.