Charlie: It shouldnt cause an issue because the CPW engineers dont have high enough access on the samsung service system to see whats gone on. If they take it in for a software fault they will only dead-flash it, which replaces everything as it should be.
The only problem you might encounter is if it wont reflash (very rare) and it gets sent to someone like me to investigate the problem. Having said that, if you do send it in and are conerned, keep a note of the imei and pm me with it so i can sort it out.
If you do bugger it up, use the emergency recovery in kies to reflash it before you send it in.
One other thought - if you ask a CPW engineer what "root" is they are liable to reply "thats what the bottom of a tree is called, isnt it?"
