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A gotcha I can think of is that the agency controls when your invoices are raised. If you want to raise an invoice (say) in the last tax year or vat period or delay it a few days so it's in a different one then you can't do that with self billing (probably a minor point if your cashflow is reasonably smooth).
The biggie in my mind is that if your agent promises to pay 30 days after the invoice date then as far as I can see, the invoice date is the date that they choose to raise the self billing invoice.
A workaround to this is to make sure they are contracted to pay you within X days of submission of a timesheet. Though this then conflicts with the agency regs (if you are not opted out) because you are supposed to be able to bill them even if the client hasn't signed your timesheet and I can't see how this would work with self-billing.
A few people said to raise your own invoices. I don't think this is correct though I can't find a reference for this off the top of my head. I think the rule was that if you are on self billing then the customer (eg agency) raise the invoice and you are not permitted to raise one too. That doesn't mean that you can't raise some sort of invoice for your own records, just that it is NOT a VAT invoice and you shouldn't send this to anyone.
The other thing with self billing is that if MyLTD raises an invoice then the agency has to check it against the timesheets to make sure it's for the correct amount. If the agency raises the invoice for you then it's YOUR responsibility to check that they have invoiced for the correct amount. Mistakes do happen and self billing moves the burden of checking from the agency to you. I just keep a spreadsheet with a one liner showing what each of my invoices should be and double check this against the self-bill invoices, issued date and payment date when they arrive. Easier than creating having hundreds of your own invoices to trawl through.
Free advice and opinions - refunds are available if you are not 100% satisfied.
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