You need to instruct the stream to either append or overwrite the contents of the file...
Take a look at FileOutpuStream(File, boolean)
for more details
Updated
After some mucking around, I found that the only solution I could get close to working was...
RandomAccessFile raf = null;
try {
raf = new RandomAccessFile(new File("C:/Test.txt"), "rw");
raf.seek(3);
raf.writeBytes("BB");
} catch (IOException exp) {
exp.printStackTrace();
} finally {
try {
raf.close();
} catch (Exception e) {
}
}