Occasionally delete your base engine DerivedDataCache, as it gets big

The folder to delete:
Editor Install Drive Letter > Users > Your Username > \AppData\Local\UnrealEngine\Common\DerivedDataCache

After doing this, the first time you open up .uproject files, they will recompile shaders and store them in the cache folder.

You can change the path to the folder (if you'd want to change disk letters or have it default to something like C:\DeleteOccasionally) by opening up BaseEngine.ini and modifying line 2418 (on 5.3 at least) to change the base path for the DDC.