Something to note is that the requirement to get UKARA is to have played a minimum of three games over a minimum of 8 weeks.
But there's no maximum time in which you have to do these three games. Specifically, there's nothing in the UKARA rules about having to do them within the same year.
So if you've done three games at one site, even over multiple years, then they could notionally assign you a UKARA number. It's entirely up to them - you'll need to ask the site.
Two tones aren't the end of the world though. If you do decide to paint or strip one, well, that's an offence, but the defence is airsoft use. So if you can show that you have played, and - I'd suggest more importantly - that you have a future session booked, then I'd consider that as much of a defence as a UKARA number which only speaks to your past behaviour, not the intended purpose of the modification.