Shop checks not clearing with mystery free standing items

if the mystery free standing item setting is enabled shop checks don't seem to properly clear even when the item is bought. Problem also occurs for non mystery items in this setting if the item is not a single time purchase. This causes available checks and total checks to reflect incorrectly

Reproduce the issue with mystery free-standing items enabled, including a non-mystery item that can be bought more than once. Trace the shop-check handling from the purchase path and compare available and total check counts before and after buying the item. Done means both counts clear or update correctly for each affected item type.

Written by the indexing model from the issue text.