This is annoying and it happened to me before as well. Unfortunately there are a lot of different reasons why this can happen. Here are just a few thoughts/steps to try:
When removing the Add-On (click on yellow warning sign, then remove button becomes active), make sure to also close the Add-On manager with OK. Only after closing the Dialog with OK the Add-On is really removed.
Clean the build folder and regenerate the project with CMake
Make sure to use the correct build target in XCode
The file AddOnResources.stamp.rule is generated by CMake (or XCode when building from a CMake generated project), so that's why it might show up as changed although you don't change it manually.