Since you haven't provided any code I can't give you a definitive answer, but ASTRewrite does work even if it is used outside the Eclipse "ecosystem".
Most likely you are using the wrong method to apply the changes on the AST.
In order to make it work, do the following things
Read the whole java file into a string and create a org.eclipse.jface.text.Document from it
final String source = FileUtils.readFileToString(javaSRC);
org.eclipse.jface.text.Document document = new org.eclipse.jface.text.Document(source);
Now you can create an instance of the ASTParser and ASTRewriter and setting the source of the parser the document you just created.
ASTParser parser = ASTParser.newParser(AST.JLS4);
parser.setSource(document.get().toCharArray());
parser.setKind(ASTParser.K_COMPILATION_UNIT);
final CompilationUnit cu = (CompilationUnit) parser.createAST(null);
ASTRewrite rewriter = ASTRewrite.create(cu.getAST());
cu.recordModifications();
After you have finished with all the modifications, call the proper rewrite method which is : public TextEdit rewriteAST(IDocument document,Map options)
After this you can apply the changes and (if you wish) write back the changes to the file as well.
TextEdit edits = rewriter.rewriteAST(document,null);
edits.apply(document);
FileUtils.write(javaSRC, document.get());
Btw: I have tested this code with the following jars:
org.eclipse.osgi_3.8.2.v20130124-134944.jar
org.eclipse.jdt.core_3.8.3.v20130121-145325.jar
org.eclipse.equinox.preferences_3.5.1.v20121031-182809.jar
org.eclipse.equinox.common_3.6.100.v20120522-1841.jar
org.eclipse.core.runtime_3.8.0.v20120912-155025.jar
org.eclipse.core.resources_3.8.1.v20121114-124432.jar
org.eclipse.core.jobs_3.5.300.v20120912-155018.jar
org.eclipse.core.contenttype_3.4.200.v20120523-2004.jar