I'm not sure what the idea is, here.

First off, you don't need to edit the airfile to add repaints, you need to edit the aircraft.cfg file.

Why would you want to simply replace all these files?  If you do, any repaints you have made would be overwritten by the new ones.

Exactly how many repaints are we talking?  If its less than 20, you should be doing it all by hand anyway.  I agree that it is time-consuming and a bit tedious, but a great many errors can be built up by having a program do it for you.

I also prefer to see what I'm adding to my aircraft configs, as this allows me to specify all the little options that are available.  95% of the time, I will change the names the aircraft are listed under to suit my own needs, as I have a weird way of listing them.

If I were you, I would really take a few minutes to sit down and go through all the repaints and make sure each one has the right stuff to be added to the aircraft config.  I cannot count the number of times I have gotten a download and found that the names (and sometimes the rest of the [fltsim.x] entries) were missing or wrong.