I've done many mods. Will they still repair unrelated stuff?

[Blackthought_]

My car has been at the dealers for 4 weeks to date, the ECU kept the data of the problems and when they occurred, they could see that there's a gap in ECU data.

I would say change the ECU as they will connect it up to check for updates, obviously a non Lotus ECU won't take the updates. Paint is clearly not connected to the upgrades so can't see a problem with that.

Even if you plug in the stock ECU before bringing it in to the dealer, I guess the question is if they see a gap in the ECU, will that give them incentive to say sorry this issue is not covered by warranty