Editing Javascript using Chrome Developer Tools
I know this question is stale, but I just had a similar problem and found the solution.
If you have the file prettified, Chrome will not allow edits. I turned it off and was able to edit. Willing to bet this is/was your problem.
You can edit javascript in the developer tools on the "Sources" tab, BUT it will only allow you to edit javascript in its own file. Script embedded in an HTML (or PHP) file will remain read-only.
It has some limitations:
has to be a JS file. can't be embeded tags in a html page.
it cannot be prettified.