"Good fences make good neighbors" is an English saying that clear appointments make it easier to be on friendly terms with someone. This is exactly the reason why changing borders is so risky: everything has to be agreed again. Putting minority rights on paper helps only a little bit. You cannot legislate discrimination and contempt. After some time in most cases there develops a kind of mutual respect but that takes time and sometimes involves confrontations.
However, once you are changing borders everything is in play. The Western countries are still pretending that blowing up Yugoslavia was not the changing of borders but they are just deceiving themselves and trying to deceive the rest of the world. What they did put all ethnic relations in play and made it necessary to find new power balances and new ways of living together.
In such unstructured circumstances it is a matter to find a structure as soon as possible. However, as long as there are open points of conflict this will be difficult, although not impossible. That implies that subjects for conflict should be minimized. The first and most simple way to do this is to apply ethnic borders. This reduces the risk for long time border conflicts and also conflicts about the government trying to impose its will in the minority area - often involving efforts to change the ethnic balance. Next is to settle all conflicts as soon as possible. Kosovo's thousands of real estate conflicts for example should have been settled long ago with some special procedure. Similarly perpetrators of crimes against the other ethnic group should be convicted fast: the punishment might be somewhat lower to compensate for a less careful procedure as usual.
For that reason I have already often repeated that the rule should be: "Don't change borders, but if you do it do it good". That is: take into account ethnic borders and other practical considerations so as to minimize the number of inherent conflicts.