Emailed the Shropshire CIL team and the next day received the following:
"When you submit CIL Form 7-2, I would advise you provide a copy of the letter you would have received from HMRC to confirm they have received your claim. That way, I will be aware you are trying to obtain confirmation of a DIY housebuilder VAT refund. You can then provide the confirmation letter when you do receive it. If the confirmation letter is not forthcoming close to the 6 month deadline, a potential extension can be discussed since this would be due to circumstances beyond your control. "
So thanks Newhome for the suggestion.