Delete One Submodule will Delete all visible submodule entries of a repository.

Delete One Submodule will Delete all visible submodule entries of a repository.

Steps:
-Add Two different Submodules to a Repo
-Delete One of them with right click delete or by removing the submodule entry by hand from .gitmodules
-see all othervisual entries are gone

Solution:
You forgot to call:
-git rm --cached "full path"
(Example: -git rm --cached Unity/dllProjects)

Doing so is the clean way and will solve the problem/symptome

http://stackoverflow.com/questions/1260748/how-do-i-remove-a-submodule

You may want to Open Source SourceTree. I use it a lot and would solve those bugs in minutes.