I am having the same issue. The weird thing is that it is not consistent. The inventory is tracking correctly as the note feed clearly shows the correct sku of the variation but the line item shoes the parent. This is providing to be a problem when exporting invoices to QBO as the parent SKU really is not a product at all and it is not part of the inventory. Anyone has a solution?
disabling via FTP the plugin, simply by renaming the folder, made the site come back online. Then i updated to 1.2.40 and enabled and everything is working again.. not sure what happended.
