Prelude CC 2017 (6.1) introduced a new feature to manage and automatically remove aging and unnecessary media cache files. This feature was designed to assist users in managing existing project media cache files more easily. In the default location for media cache preferences, there is no issue. However, incorrect usage of this feature has the potential for unintentional file deletion.
To avoid this issue update to Prelude CC 2017 (6.1.1).