Duplicate GUIDs if using a project group

I have a project group with all FNC projects in order to to build and install them fast after each update like in the photo:


I install them as source and compile them manually as this fixes problems with max path size in MSbuild and I have installed many components in the IDE
Each time a new version update of FNC components is installed a couple of them seem not to be uninstalled and when opening the project group file I am getting a lot of prompt dialogs like the followings:
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