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This is true. Subtle differences are inescapable.I think you're going to find it hard if not impossible to accomodate every character's backstory and the travel routes taken by every adventure. (e.g. I think the route that the players took in Sojourn to Sairundan would have been rather different on your map.) So I think it's worth taking a page from L4W's book, and have your map be an in-game construct, made by an NPC, and just admit up front that it's inaccurate in various unspecified ways. Did your homeland get left off the map? Oops, sorry; buy a map from a different cartographer next time. I mean, have a look at some real-world medieval maps sometime. [1] [2] [3] Those things vary between being completely unrecognizable, and being pretty accurate for small regions, but with huge missing sections. But without airplanes and satellites and surveying tools, what else are you going to do?
[1] http://www.henry-davis.com/MAPS/EMwebpages/201A.html
[2] http://www.henry-davis.com/MAPS/EMwebpages/221.html
[3] http://www.heritage.nf.ca/exploration/port_cantino.html