You need to restore the device to factory settings in iTunes prior to taking it to Apple for diagnostics and replacement. They will honor the warranty as long as the jailbreak has been removed with the restore.
Only temporarily. We won't even touch your device if its jailbroken (unless it's physically damaged to the point that it's dead). We won't help you with wiping it either while its jailbroken so we're not held liable in case something goes wrong during the wipe.
Once the jailbreak has been removed, no problem we will service the device for you.