From what I remember, you are responsible for the bike while it is in your possession, so you are expected to bring it back to saleable value and keep it correctly maintained while you own it. In your shoes, as I presume you are intending to fix it so you can continue riding it and then buy it at the end of the scheme I'd just do the repairs and not bother mentioning it to anyone. I don't recall a requirement to inform them, but it will be in your contract which (depending on the scheme) should be available to check on line (we use the official Government sanctioned one, Cyclescheme.co.uk and they keep the contract readable on line.)
As I have intended to keep the bikes I've got through the scheme, I've not worried about modifying them from the off but by the rules they ought to be capable of being returned to the hirer in the condition they were bought (plus expected wear and tear).