PyCharm fails to inspect numpy after re-adding project interpreter

I removed my project's interpreter from PyCharm2016.3 and re-added it because it didn't realize the installation of a new package. The package in question was recognized then however now PyCharm is also flooded with hundreds of warnings/error concerning `numpy`. For example:

    numpy.sqrt
    -> Cannot find reference 'sqrt' in '__init__.py'

Before I re-added the interpreter everything was fine and no warnings were shown, so I don't see what caused the problem. (Note that `import numpy` works fine.)  
After reading dozens of other StackOverflow question I tried removing PyCharm's cache, upgrading to version 2017.1, re-installing numpy however nothing fixed that bug.  
I don't want to modify the global inspection settings nor add a local suppress comment for each such reference (because there are lots of them).

Does anyone have an idea why it stopped working (while it was working before) and how I can resolve this issue?

(I am running on Ubuntu 16.04 and I'm using Python 2.7 with numpy 1.12.0.)