If your product or variant inventory is updated within Shopify, it can take some time before Custom Pricing is able to recognize these updates. As well, there may be other apps or actions taken on the site that cause this inventory to become out of sync.
However, manually syncing the inventory within Custom Pricing updates the app's inventory numbers immediately.
To manually sync inventory in Custom Pricing, while using the Variant Dependant Method, please follow these steps:
From within Custom Pricing, select Settings, then General.
Select Manually Sync Inventory.