This error is caused because Drupal keeps an internal registry of all of the files of the system, modules, themes etc. If it can't find some of these files, you will receive fatal errors and the registry is borked.
Luckily, fixing the registry is quite easy with Registry Rebuild.
Registry Rebuild is a downloadable Drush command that is packaged as a module for an easy download.
The project page also has the instructions on how to use it without Drush.