Just a little update. I didn't need to redo the whole project. I copied the contents of the problem script then delete it, then I closed/reopen the project and created new script with the same name and pasted back the content. It then asked to reload once and no more pop up 🙂
ps - As you guys said, the problem came about because I viewed the script on notepad while the project was on. I might have updated and saved the script as well, so don't do that.