Hi Mahlon,
When you delete an entity in Method that has been posted to QB, the entity record is archived and marked for deletion. Once the sync completes and the entity is removed from QB, it is then completely removed from Method along with any related contact records.
When a lead is deleted, since it does not sync with QB, it should be removed immediately along with any related contacts. There is a ticket with the development team, as this is not happening as it should. At this time, I believe that the lead is being archived, marked for deletion and the related contacts are remaining in the Contacts table.
Keeping in mind that there is a ticket for lead contacts not being removed, are you experiencing different behaviour and if so can you explain?
-Audisho