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In most cases, you would just input the invoice into QuickFile. It’s not necessarily an actual invoice, but just a way of recording your income and VAT accurately. If it’s another system that’s generating the invoices, such as a till system or e-commerce site, then you can bulk record these, which should hopefully answer points 1, 2, 3 and 4. There’s more relating to bulk sales in these two topics:
Regarding point 5, QuickFile doesn’t support multiple styles of invoices as normal. You can create trading styles which allow you to have a number of different invoice templates, but this is tied to the client and not on an invoice-by-invoice basis. I have however included a link to this below for reference:
Since the company is going to use both QuickFile and an external system for creating invoices, with your proposed approach some entries will have double invoices with different invoice numbers. One in the external system and one in QuickFile.
Is this allowed? How to handle such situations during potential inspections?
Providing you have the backing data to go with it, recording bulk sales is acceptable. If there was an inspection, it would be the source of that data (the backing reports) that HMRC would want to see.
Providing everything is easy to trace, you should be fine. For example, enter your weekly sales as Website Sales for w/c 04/12/2017 rather than just Weekly Sales would help. I would also be inclined to suggest that you differentiate the invoice numbers, even if it’s a different prefix for your shop or website compared to this issued via QuickFile.
However, if you want to be sure, I would double check with your accountant (I’m not one) or HMRC themselves. And of course, ensure you follow their guidelines.
To avoid such situations, for the future I would propose a feature where sales transactions can be tagged to an external invoice or receipt, which can be uploaded to QuickFile. Very similar to the way purchases are tagged at the moment.