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As long as you existing rotors are in good condition and thicker than 1.6mm (minimum safe thickness) you should have no issue with using them with the Shimanos. There doesn't seem to be an industry standard specification for rotor thickness but it is generally taken to be between 1.8mm - 2.0mm. The new callipers will self adjust to the rotor width. Clean ...
From your install manual, the "Burnish" period is only 30-40 stops, so you should be beyond that. If the bike is still within a month or two of purchase, I would suggest taking the bike back to the shop and playing dumb. They sold you the bike, they should fix the brakes that aren't working properly. If they say, "they're supposed to do that", I'd suggest ...
I can't imagine how it did it as I didn't think there would be enough clearance between calliper and rotor, but the actual problem now I have gotten around to pulling off the back wheel is that the mobile pad got thrown and hence no fluid leak just a missing pad. @zenbike thanks for answer however.
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