1. remove all copies of the desktop entry from the system
sudo find / -name 'jetbrains-pycharm.desktop' -deleteprettyPrint(); (or skip the -delete option if you want to rm the files manually)
2a. if you lost track of where to manually open PyCharm,
sudo updatedb && locate pycharm.shprettyPrint(); 2b. open PyCharm manually
/path/to/pycharm.shprettyPrint(); and use Tools > Create Desktop Entry to create a new, working desktop entry. The "for all users" option is not necessary unless you really have multiple pycharm users on your system.
3. pin the new desktop entry to the launcher.