Adding Incrementing Citation ID - google-apps-script

Question

I've tried searching the issue and came up with nothing, so I'm looking for help.
What I'm trying to do is add incrementing IDs to individual citations by:
Searching a Google Doc for a specific combination of characters that signal the end of the citation (checking to see if there are any in the document at all).
If the characters are there, I'd like to find the first one, then place a '1' in between the two characters. Then the second one should have a '2' between it, the third should have a '3', and so on and so forth ensuring that all of the sets of characters have been replaced with unique number IDs
What is going wrong currently:
Due to the elemental structure of the Google Doc, my script is replacing ALL instances within a paragraph with the same ID number, which can be 1 instance or it can be 20. When it moves to the next paragraph, every found instance of the character combination is getting the incremented ID.
I need a genius' help.
Here's the code base I've found that I've been struggling to modify:
var doc = DocumentApp.getActiveDocument();
var body = doc.getBody();
var foundElement = body.findText("]]");
var i = 1;
while (foundElement != null) {
// Get the text object from the element
var foundText = foundElement.getElement().asText();
// Where in the Element is the found text?
var start = foundElement.getStartOffset();
var end = foundElement.getEndOffsetInclusive();
// Change the text
foundText.replaceText("]]","]"+i+"]");
// Find the next match
foundElement = body.findText("]]", foundElement);
i++
}

Answer 1

Issue
replaceText() will replace all the occurence in the element.
Solution
To avoid this, you should use the start and end to delete and insert text.
Please see my code below. This worked on my end.
var doc = DocumentApp.getActiveDocument();
var body = doc.getBody();
var foundElement = body.findText("]]");
var i = 1;
while (foundElement != null) {
// Get the text object from the element
var foundText = foundElement.getElement().asText();
// Where in the Element is the found text?
var start = foundElement.getStartOffset();
var end = foundElement.getEndOffsetInclusive();
// Change the text
foundText.deleteText(start, end)
foundText.insertText(start, "]"+i+"]")
// Find the next match
foundElement = body.findText("]]", foundElement);
i++
}
As you can see, I just modified the line where you replaceText() and transform it to a combination of deleteText() and insertText() methods.

Answer 2

Try this:
function myfunction() {
var doc = DocumentApp.getActiveDocument();
var body = doc.getBody();
var foundElement = body.findText("]]");
var i = 1;
while (foundElement != null) {
var foundText = foundElement.getElement().asText();
var start = foundElement.getStartOffset();
var end = foundElement.getEndOffsetInclusive();
foundText.replaceText("]]", "]" + i++ + "]");
foundElement = body.findText("]]", end);//Modifed this and the end point of the last search. And the i++ will use the i as it currently is and then increment it after the current operation.
}
}
Each next search needs to start searching after the location of the preceeding element. range element getEndOffsetInclusive()