As an auditor, I don't see why this would be an issue. What we look for is sequential numbering and the ability to trace invoice 1 through to invoice xxx.
So you could have the following hypothetical scenario:
Project A:
Invoice No's: A001 - Axxx
Project B:
Invoice No's: B001 - Bxxx
You should definitely start the first invoice as 1 though, so what ever the string of characters you put together, start it at "1" ... it will make it easier from an Audit point of view to keep track. For example, if you start it at "2", say A0002 - Axxxx ... you are going to get a lot of questions as to why "1" wasn't there.
The most important aspect of this is sequential numbering ... each invoice number system (for each of project invoice numbering) should be in a sequential number order relative to itself ... so that if I as an auditor see A014 and A016 ... I would expect A015 to be there and to be in between the times and dates of invoice A014 and A016.
Hope this helps ... I tend to over explain and confuse :P
Regards
Itai
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