Hi Ben,
Actually I received an answer to a trouble ticket I raised. Here's the answer from clearbooks and it works for me. It's a bit of a pain but as long as you don't have too many purchase invoices each month with domestic reverse billed VAT then it's manageable:
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Thanks for contacting Clear Books support.
I have tested it in demo and tried the following steps. Works for me and see if it gives you what you are looking for.
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Raise the supplier Invoice for £15750.18 as Goods and Services from UK supplier but 0% VAT.
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Create a journal for the VAT. Debit and Credit the VAT control for £3,150.03. See screen shot below of journal and boxes to tick.
https://s3-eu-west-1.amazonaws.com/uploads-eu.hipchat.com/36185/2368368/yxmfHTUBwek1pqu/upload.png
This then seems to fulfill the requirements of HMRC by showing the VAT in boxes 1 and 4 and the purchases in box 7. See attached a test VAT return.
https://s3-eu-west-1.amazonaws.com/uploads-eu.hipchat.com/36185/2368368/chbVFXXWz1Zb2q0/upload.png
I hope that this has been helpful. If you need any further assistance feel free to get in touch.