Last week I had an issue with my truck, low oil pressure, high automatic transmission fluid temp (truck had been parked and not running for 4 hours), rough idle, stale wouldn't rev past 1500 RPMs. Had it towed to the local dealership. They could not recreate the faults (not surprised). The tech created a case file with Toyota. Toyota said if it happens again I would have to put my truck back to stock before they could do any more diagnostics.
I asked if that meant my warranty was null and void. He told me no, just with this particular issue they want it back to stock to rule out that it wasn't my lighting upgrades, the Pro grill that doesn't come on the OR, even my Meso key fob.
Though these don't void the warrant you might want to hold onto old parts in case you have to jump through some hoops.