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Leaving marks of your passage can alert predators that a newcomer has entered their territory. Trackless boots help prevent you from making too much noise as you creep along, and they also mask traces of your passage through underground caverns to prevent your enemies from finding you. These boots are particularly valued by smugglers who work in patrolled areas.
Trackless boots are soft, well-worn leather boots with thin soles. The softness of the boots’ soles add a +4 competence bonus on Stealth checks. In addition, the boots conceal your passage much like the pass without trace spell — you leave no trail underground and cannot be tracked.
Emphasis mine. I am not certain, but Pass without Trace leaves no scent as well. Though the boots state that you leave no trail and can't be tracked, do you still leave a scent?