See here for information on this: https://helpx.adobe.com/media-encoder/using/media-cache-database.html
Quote:
A database retains links to each of the cached media files. This media cache database is shared with Adobe Media Encoder, Adobe Premiere Pro, and After Effects so that each of these applications can each read from and write to the same set of cached media files. If you change the location of the database from within any of these applications, the location is updated for other applications, too. Each application can use its own cache folder, but the same database keeps track of them all.
You can delete the Media Cache Files, but depending on your work, it may have a performance influence.