When Shiptheory pulls through your orders from Shopify, by default, the shorter reference (e.g. #1234) will be joined with the longer reference, to make the order number pull through as something like #1234-2133131313
However, if you're wanting to have this shorter number be separate, there is now a setting in Shiptheory to do this. In the Shopify advanced settings in Shiptheory, scroll down until you see the following option:
If you hit "Yes, save order name" this will then use the shorter #1234 reference separately.
With this option enabled, it also gives you some more flexibility with features like the Address Only Labels. If you're wanting to be able to display this short reference separately on the address only labels for your barcode, this can be done by selecting the shown option in the Address Only Labels settings:
If you have any issues there, or want to enquire into the further functionality of this, please Contact Support