Will A Rechip/remap Affect My Skoda Warranty?

Yes it does and no it doesn't. Anything that goes that could be related to the mod, would be invalidated, but not anything else. It is also worth saying here that Skoda UK (or any VAG company) will not approve ANY chip.

Also, it seems dealer dependent, some ignore knowingly others won't.

Anyone, engineer or assessor, could tell (if they knew what they were looking for) if a car has been rechipped by opening up the ECU. If you want to hold it back from the insurance, that's your choice, but personally, I'd never take that risk - the cost of being refused a large claim would be horrific. Remember, you've got a performance car and these companies aren't all stupid - they may know to look for mods, especially as 1.8T tuning is getting extremely popular.

A couple of chip manufacturers offer underwritten warranties that run alongside the Skoda warranty and will repair any damage deemed to have been caused by the chip (inspected by an independent assessor).

Weigh it up and take your choice, it's all about balance of risks. If you're too worried then best leave it alone. Chips are made to well within engine tolerances but things can go wrong from time to time, although not usually related to the chip. If you are the type to worry endlessly about worst-case scenarios, just enjoy your standard, and still fast, car.

If you can't pay, don't play.......