I do think mould could have contributed to Charlie’s problems. He is young, I dont know how old Pip is, but young animals are as a rule more sensitive due to their immune defense not yet being fully mature.
That said, longer courses of abx and combinations/change of types of abx during the course of treatment is not at all uncommon with rabbit sinus infections.
The problem with sinus infections is often that the infection causes the mucosa in the sinuses and nasal cavity to swell, thus narrowing the already narrow passages. This creates ideal conditions for bacteria to form biofilms, where some of the bacteria can go into a resting, “hibernating” state, while others keep diving. Most antibiotics target dividing bacteria, and won’t affect the dormant ones. So the dormant ones are spared, while the actively dividing ones get killed off – and when the course of abx is over, some of the “sleepers” wake up and start to divide and the symptoms return.
This means you get a period when the animal seems fine for some time – and then you get a flare-up.
When we humans get a sinus infection, we can use corticosteroid nasal sprays to reduce the swelling of the sinus-and nasal mucosa. This is often very effective, so that we only rarely need to take antibiotics. With rabbits, corticosteroids are unfortunately not an option. Corticosteroids should only ever be used in rabbits as a very last resort for life-threatening instances of inflammation, most commonly seen with really bad bouts of e cuniculi.
It is however very positive that you have identified a mould problem so you can deal with it properly. It will undoubtedly be of great benefit to the whole family.