I’ve been running into this issue a lot recently when dealing with virtualenvs with my Python projects. (Which forms the majority of my work, so it’s definitely not just a minor concern.) I’m planning on writing a post on why working with virtualenvs for me is so important these days, especially when dealing with larger projects that could span multiple working environments, and especially more so when you need to collaborate with others as well. But that’s outside the scope of this post for now.
Essentially, as shown above, sometimes PyCharm will, for whatever reason, decide that the best solution for you adding a new Python interpreter is to add it as a duplicate entry. Removing any one of the entries then results in all of them being removed. Re-generating the caches, removing the project and re-adding it, un-registering it as a VCS root…every action via the GUI as far as I can tell is unable to resolve the issue.
To solve this, go to your PyCharm user configuration folder in $HOME/.Pycharm40 and open the jdk.table.xml file located there. (e.g. C:\Users\sonictk\.PyCharm40\config\options\jdk.table.xml)