It's not the shop's warranty, it's Cannondale's that's voided by this.
No worries about it; the extra travel of the fork will cause no noticeable 'extra wear' on the frame. My Jamis Dakar XLT was designed to accept a 130mm fork, and I've had a 145mm on it for over 3-1/2 years, still rides like new.
Using Stan's solution in a Kenda tire voids their warranty, too; bet you can't find too many people who have been stopped by that.
Cannondale may well make a good bike, but I hear more and more lately about issues with them backing up their products; may have something to do with Dorel, the parent company (Canadian children's furniture company, also owns Pacific Cycles, owners of Schwinn/Mongoose/Roadmaster, the bane of existence at Wal-Mart).
If the bike rides OK, ride it til it dies, then get someone else's creation. (I hear Jamis is pretty good, LOL!)