Changing values in XML when looping not saving the new values on next loop

Question

Hey all I am having an issue with the code below due to me not being able to grasp what I am missing. I know the issue is that every call to searchXML() it just reads the original file that does not have the edits in it. But I am at a loss as to how to go about using the original and then not using the original since my attempt below does not seem to work....

static int X                        = 0;
public static void main(String[] args) {
    String[] tags = {"<!--D01-->:2000-12-08",
                     "<!--D02-->:2010-01-02",
                     "<!--D03-->:1990-02-29",
                     "<!--D04-->:2015-09-12",
                     "<!--D05-->:1996-04-04",
                     "<!--D06-->:2002-05-22"};

    try {
        for (int i = 0; i < tags.length; i++) {
            searchXML(tags[i], tags.length);
        }
    } catch (Exception e) {
        e.printStackTrace();
    }
}

public static void searchXML(String TAG, int MaxNumber) throws Exception {
    Scanner input                           = null;
    String modifiedXML                      = "";
    String theText                          = "";
    String currentLineValue                 = null;

    // Split array into 2 separate values [0]xxxxx [1]zzzzz
    String[] _tmpSplit                      = TAG.split(":");

    if (i >= 1) {
        //We've been around 1 or more times (load modified xml file)
        input = new Scanner(new File("c:/temp/newXML.xml"));
    } else {
        //We've been around only 1 time (load original xml file)
        input = new Scanner(new File("c:/temp/anotherxml.xml"));
    }

    while (input.hasNextLine()) {
        currentLineValue                    = input.nextLine().trim();
        currentLineValue                    = currentLineValue.replace("<!-- ", "<!--").replace(" -->", "-->");

        if (currentLineValue.contains(_tmpSplit[0])) {
            modifiedXML                     += currentLineValue + "\n";
            currentLineValue                = input.nextLine();

            //check if this is just a blank tag
            int blankTag                    = currentLineValue.indexOf("</");

            if (blankTag == -1) {
                //Its blank so go to the next line
                modifiedXML                 += currentLineValue + "\n";
                //Now grab that new lines text (that we wanted originally)
                currentLineValue            = input.nextLine();
            }

            //Check for the position number of where the > ends
            theText                         = currentLineValue
                                                .substring(currentLineValue
                                                    .indexOf(">"), 
                                              currentLineValue
                                                .indexOf("</"))
                                                    .replace(">", "")
                                                        .trim();

            //Now replace the old value (_tmpSplit[1]) with the new value (theText).
            currentLineValue                = currentLineValue.replace(theText, _tmpSplit[1]);
        }

        //Finally save the modified value (if...) or original value (else...)
        modifiedXML                         += currentLineValue;
    }

    input.close();
    X++;

    //Format and save new XML to file if we reached X
    if (MaxNumber == X) {
        Scanner input                       = new StreamSource(new StringReader(modifiedXML));
        StringWriter stringWriter           = new StringWriter();
        String pretty                       = null;

        try {
            // Format the 1 row string XML we made into pretty line(s)/tab(s) xml
            Transformer transformer         = TransformerFactory.newInstance().newTransformer();
            transformer.setOutputProperty(OutputKeys.INDENT, "yes");
            transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "no");
            transformer.setOutputProperty(OutputKeys.METHOD, "xml");
            transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "2");
            transformer.transform(xmlInput, new StreamResult(stringWriter));
            pretty                          = stringWriter.toString();
            pretty                          = pretty.replace("\r\n", "\n");                         
        } catch (Exception e) {
            throw new RuntimeException(e);
        }

        // Write the new xml file
        BufferedWriter writer               = new BufferedWriter(new FileWriter("c:/temp/newXML.xml"));
        writer.write(pretty);
        writer.flush();
        writer.close();         
    }
}

anotherxml.xml = the main xml file that needs changes.

newXML.xml = the new xml file that has the changes.

If someone here can wrap their head around this and let me know what I would need to do in order for it to..

Be able to read the old xml.

Loop through that to find the X number of replaceable values.

Save the new XML with that value.

Go to the next value we are looking for.

This time around it loads the modified xml.

repeat.