File editing program
Actually, this can be more generic.

Instead of hard-coding your map; fill it from your properties file.
So change your prop file to : 

#db.id=a
#db.user=testa
#db.password=testa

db.id=b
db.user=testb
db.password=testb


Fill your map like this :

private Map&lt;String, String&gt; schemaMap = new HashMap&lt;String, String&gt;();

public void fillMap() throws FileNotFoundException, IOException {
    String line;
    String key = null;
    String value = null;
    try (BufferedReader file = new BufferedReader(new FileReader("test.properties"))){
        while ((line = file.readLine()) != null) {

            if (line.contains("db.id")) {
                key = line.substring(line.indexOf('='));// could be you have to do an + 1
            }
            if (line.contains("db.user")) {
                value = line.substring(line.indexOf('='));
            }
            if (key!=null &amp;&amp; value != null) {
                schemaMap.put(key, value);
                key = null;
                value = null;
            }
        }
    } catch (IOException ex) {
         // report with Logger or System.out what happend.
    }
}


Secondly : In your main you use the args.
You do not check for how many args you have, you just take the last arg.
Maybe a check for how many args you have is appropriate here, and make the program do what you want then. (like quitting with error message or taking default arg).

Third : Always close your resources(reader/writer in this case).
Here it is done with a Try-with-resources available from java 7, otherwise you will need a finally block where you close it in.