Was the change in area a decrease or increase? Were there any other changes that you noticed? Per your post, the 'shutdown and restart' seem, at least to you, to be involved in this change. Was there anything that precipitated this event? Did something cause you to need to restart the instrument? Did you notice anything odd before or after the restart? Have you re-prepped and re-run standards and compared them to previous injections to determine if this change in area is a one-time event?
If you had, for instance, a power outage, and you had not saved some important changes to a method (specifically, injection volume), then upon restart the instrument may have loaded the old version of the same method you had been running, but with the previous injection volume (say, 100 uL vs. 20 uL). Just a thought. You may want to check each parameter to make sure it really is "the same as" before the shutdown.