Many travel agents advise clients they can view their itinerary online at checkmytrip.com or virtuallythere.com or other such site, it's quite normal practice and that is the reason why these sites exist. The GDS promotes them as such.
However, it is still the travel agents job to notify the client of a schedule change. The PNR will show any schedule changes by the airline and the old times and new times.
There is something very strange going on here as others have noted checkmytrip simply looks at the PNR and current schedule directly from Amadeus... so there is no reason why the flight time would be wrong. Someone has made an error somewhere along the way, are we looking at a case of am/pm here?