The problem was that I had the settings icon in the dock. Badge clear doesn't work when you try to clear the notifications when the app is in the dock. Thanks for the info and help 👍
I just used No Update. i still had the badge after that, but thanks to Springtomize 2 I just enabled 2 tap clear in the "Icons" section, and once I removed the badge once it has never come back. No popup either. just place icons in edit mode, and double tap any icon that has a badge on it.