Right then chaps, sorry I didn't post yesterday but council sparks came out Monday and got to the bottom of it. Bottom line is, it was a loose neutral causing the fault in 3 lights.
So, to talk through the actually wiring of it, all lights on the bank are fed from a single switched line, with the exception of 2 & 5 that have an additional perm line for emergency. Lights 1-3 are fed by 1 neutral, lights 4-6 are fed by another totally separate neutral (independent all the way back to the board). Other banks are seemingly wired the exact same, 1 line 2 neutrals, so this looks original wiring instead of bodged repair. The loose neutral was at a junction box upstream from lights 4-6, hence why only these 3 lights were faulty.
So, I got a belt, and I think the reason is, I separated the neutral after light 3, what I thought was the link from 3 to 4. Because I'd left the emergency connected and had only isolated at the switched line (wrongly thinking light 2 was upstream and therefore wouldn't be affected by me breaking the neutrals). Instead of breaking 3-4 neutral link, I broke 3's neutral back to the DB and hence the belt. Yep, it's my own fault - safe isolation would have prevented it, and I've learned a massive lesson.
However, anyone know why it may be wired in such a way?