Clion doesn't notice changes in pkgconfig files

I made a change in a /usr/local/lib/pkgconfig file (a file thath cmake uses to determine the libraries to link).
Using cmake on the command line worked (it noticed the changes), but CLion did not, even after deleting and recreating the project.
Only after deleting ~/.clion/ did it pick up the changes. It must cache some information there that needs to be refreshed.

Am I missing something here? Is there another way to refresh the cmake build, or should I report this as a bug?