Changing the encoding in Eclipse does not change your existing files: it only changes the way you read Eclipse.
You need to convert the old files to UTF-8, as well as configure Eclipse.
There are several tools for this, and you can write a small java program.
, , : http://www.marblesoftware.com/Marble_Software/Charco.html ( () .
( 20 LOC), , :
:
reader = new BufferedReader(new InputStreamReader(new FileInputStream(...), "you have to know it"));
writer = new OutputStreamWriter(new FileOutputStream(...), "UTF-8");
String line;
while ((line=reader.readLine())!=null) {
writer.write(line);
}