By default, whenever you upload a new print file to an existing product, the product gets republished and all the setup gets reset to default.
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To prevent this from happening, please visit your Supliful account Settings by clicking on your Avatar bubble first:
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Then scroll down to Advanced Settings. Tick the checkbox next to "Prevent Shopify product update on print file change" and click Save.

That way your Shopify product listing will not change, but we will use the new print file to fulfill your orders.