Parse the file as a string, then find char position of the second to last line return, substring from 0th char to 2nd last CR/LR (removing bottom line), and append this substring to the line you want at the top...?
oldFile >> originalString;
substring = originalString - last line;
newString = newText + substring;
newString >> newFile;
I think this will work, it's been over half a year since I last used java so I may be a bit rusty. (There are probably better ways of doing this also.. )