Just to take a dissenting point here, but, there is a point where, if you are changing large swaths of setting canon, it could be said that you aren't really playing in that setting anymore. Where that point is, I don't know, but, I can honestly say that if a DM said, "Hey, I'm running a Scarred Lands campaign" and then changed nearly every detail other than the maps, I'd be a bit surprised to say the least.
Vigil's of Vesh were mentioned earlier. Fun group - a bunch of fairly nice guys out to save the world. Great. However, if the DM decides that the Vigil's of Vesh are now demon worshippers out forcibly converting all and sundry to the worship of Orcus, then I wouldn't mind at least a heads up on this beforehand. If your Calastian army is roving around in air ships armed with mystic cannons, that's probably something that should get pointed out beforehand. If the council of 13 dragons in Albadia decides to invade Darakeen to remove the evil Lich Queen of Darakeen, then I'm going to wonder what's going on since SL doesn't have dragons and Darakeen doesn't have a Lich Queen.
If all of the above are true in your campaign (using the general "your" here), then I'm going to say that you are not running a Scarred Lands campaign. It might share the names and the map, but, it's not an SL campaign.
There is a happy medium here.