If you have a store and you override it for a given segment, if you delete the store that you override, the relationship is not cleared in the parent store.
If you have Store ID "A", and you override that store for a given segment say "Big Spendahs", with the contents of Store ID "B", then you delete Store ID "B" and export Store ID "A" as JSON, Store ID A still has the segment definition "Big Spendahs" defined in the JSON, which blocks import if "Big Spendahs" doesn't exist in the target environment you are importing