Hi @j-bruce-wkca-co-
C79 Certificate is like a receipt from HMRC - usually for VAT paid direct to HMRC but, in certain circumstances, they can be generated when the VAT has been paid via a third-party (an import courier, for example).
To avoid claiming twice, you need to check whether the VAT it relates to was paid direct (since PVA was re-introduced that would be unusual).
If it was paid direct, you can enter into QBO as a Bill - 100% VAT.
If it was paid to a third-party, you should have their Bill showing the VAT element. Pin/Attach the C79 to this Bill as your evidence for VAT reclaim.
Hope this helps.