In the rgn files, you get an entry called 'Name'. This is the display name of the region, and is not the entry used to generate aliases for regions (which are tricky to changes, as they are used in many places in the database).
You can safely rename the display name without adverse effect. Problem is that if you want to do some mass renaming, like Aryaman need to do in his Punic War Mod, you would have to open and save thousands of files.
So here is the solution, an utility we did for that:
http://ageoddl.telechargement.fr/latest/RegionsUtil.rar
Operating procedure:
1 - Edit the Regions.XLS of the game of your choice, column B, Name.
2 - Export to CSV
3 - Launch the utility
4 - Indicate the directory where rgn are, and where is the CSV.
5 - Click on Process (the result is almost immediate)
Please note that this column is used to generate the aliases for regions when the database is first created and that you don't want that change necessarly (as this is a bit of a pain to alter regions aliases, when the database is consistent and running correctly). So it is better that you alter these names in a duplicated Regions.xls file, used only to alter this column for the purpose of changing the Display Names.
Last, aliases are never mandatory. You could always use the numerical equivalent of it. So if you prefer, you can use the value 0 instead of $Donegal in NCP eg.