Eclipse AST not changing files which are not opene

I am trying to modify source code using eclipse plugin, JDT and AST (Abstract Syntax Tree). I can read all Java files and make operation on all those file, But when i am saving those changes (Edits) in to files using

    TextEdit edits = rewriter.rewriteAST();
    // apply the text edits to the compilation unit
    edits.apply(document);
    iCompilationUnit.getBuffer().setContents(document.get());

It only make changes in file those are open in eclipse in unsaved mode. Rest of files are not affected.

Find my code snippet below:

CompilationUnit cu = parse(iCompilationUnit);
    MethodVisitor visitor = new MethodVisitor();
    cu.accept(visitor);
    String source = iCompilationUnit.getSource();
    Document document= new Document(source);
    ASTRewrite rewriter = ASTRewrite.create(cu.getAST());
    cu.recordModifications();
    for (MethodDeclaration methodDeclaration : visitor.getMethods()) {
        System.out.print("Method name: " + methodDeclaration.getName()
                + " Return type: " + methodDeclaration.getReturnType2());
        MethodDeclaration methodDecl = methodDeclaration;
        Block block = methodDecl.getBody();
        ListRewrite listRewrite = rewriter.getListRewrite(block, Block.STATEMENTS_PROPERTY);
        Statement placeHolder = (Statement) rewriter.createStringPlaceholder("System.out.println(\"Test Print\");", ASTNode.EMPTY_STATEMENT);
        listRewrite.insertFirst(placeHolder, null);
    }
    TextEdit edits = rewriter.rewriteAST();
    // apply the text edits to the compilation unit
    edits.apply(document);
    iCompilationUnit.getBuffer().setContents(document.get());

Try to:

Apply the TextEdit directly to the ICompilationUnit instead of using Document.
Use ICompilationUnit.commitWorkingCopy to save the changes

I use code similar to this:

iCompilationUnit.becomeWorkingCopy(new NullProgressMonitor());
CompilationUnit cu = parse(iCompilationUnit);
ASTRewrite rewriter = ASTRewrite.create(cu.getAST());

... process AST ...

iCompilationUnit.applyTextEdit(rewrite.rewriteAST(), new NullProgressMonitor());
iCompilationUnit.commitWorkingCopy(false, new NullProgressMonitor());