A fork with more or less offset will change the trail at least slightly, and I suspect that any bike shop might be concerned about liability if you were to make a change — basically it will make the bike either slightly "twitchier" or else slightly more stable, but harder to turn, depending on which way you go. Whether you notice the difference at all is hard to say.
My experience re changing offset is more with motorcycles than with bicycles, but I don’t really see where 29s would be particularly more sensitive to offset changes than would 26ers.
Note that changing offset also will change wheelbase — so if you are reducing offset (and thus reducing wheelbase, you want to be sure you will have sufficient clearance — wouldn’t want the front tire to contact the down tube on full compression! Though I doubt this would be an issue.