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If you enable Shopify quantity autosync, any new merch you add to Bandcamp will be automatically synced to Shopify, so long as the SKU matches an item on Shopify.
The same is true for editing SKUs: if you’ve enabled quantity autosync and edit a merch item on Bandcamp with an SKU that matches one on Shopify, that item will automatically be synced to Shopify.
If you do not want this, then you can turn off autosync for this particular item by clicking edit item in the Synced Merch page, and from there, select Do not sync with Shopify in the Quantity & Options section. You can then manage the quantity manually.
If you don’t have the global quantity autosync setting turned on but you do have your Bandcamp account connected to a Shopify store, when you add a new merch item you can go to the Synced Merch page to select it for syncing. (In fact, you’ll be reminded of this when you save.)
Note that when an item is synced with Shopify, you cannot edit its quantity in the Bandcamp Merch editor. The merch editor will give you the inventory levels available, according to Shopify.
Working with options and variants
Bandcamp and Shopify both support “options” — things like vinyl color or t-shirt size. Shopify calls options “variants”.
With regard to inventory syncing, individual options work like any other merch item. In particular, each option should have a unique SKU and those SKUs must match across platforms. That is, the “Small” option of a t-shirt on Bandcamp will have a different SKU than the “Large” option on Bandcamp, but the SKU of the “Small” on Bandcamp will match the SKU of the “Small” over on Shopify.
If you are using the global quantity autosync setting, options on Bandcamp will be synced automatically with corresponding variants on Shopify, assuming their SKUs match.
If you are not using the quantity autosync setting and want to sync an item with options the corresponding items/variants have on Shopify, find the options and variants on the Synced Merch page (use the SKU or title filter to search more easily) and then select the Sync Inventory button for each option individually.