Now everything makes sense. I’m not an emonCMS expert, so you’ll need someone who is to help you.
But I do wonder, given the fact that you are recovering your expenses, whether you would need a guaranteed accurate reading - and for that I’d have recommended a certified meter. There are many available, DIN-rail mounting so might fit inside your consumer unit if there’s space, that are not wildly expensive, and there would be no room for argument from your firm nor HMRC. Many have Modbus so could be read from your emonPi with the addition of a RS485 serial-USB converter. Have you seen this discussion: New build house: improving on clip on CTs
One suggestion that I can make: if you do have a pulse count from your meter, you might like to put both c.t’s on the meter tail (yes, I realise it means taking the C.U. apart again) and calibrate them against the pulses. Then you’ll know the accuracy of your c.t’s.