The Process POS orders setting is enabled but stock is not deducted in Linnworks.


Check that on your Shopify back-end Mark Orders as Fulfilled and Linnworks setting Download processed orders in Settings > Channel Integrations > Edit Channel Integrations are not enabled at the same time. 

If both of them are enabled, as soon as the sale is made that order is marked processed on Shopify. Next Download processed orders setting applies to this order once it is downloaded and do not deduct stock level in Linnworks.

To resolve this, please disable the Mark Orders as Fulfilled setting in the Shopify Settings.