hi d3ko, congrats on your step up from lurker into the hallowed halls of the cartographer
There is no easy way to do what you propose, because removing a whole region from a map will of course leave a giant hole which then makes it necessary to move borders and so forth. So that would affect not only the deleted region but all regions on the map. If you put your borders in a layer of its own, you can just adjust in that layer - but naming convention for cities and lakes might be different from region to region and the new borders might change a lot of names also.
Working with many layers however is very normal for digital artists, I seldom end up with less than 50 in photoshop and often more than 100 - and in Illustrator counting sublayers and every object gets its own layer there will be thousands of layers. So the only problem there can be the capacity of the computer in question.