Do any of your plex users have the permissions required to delete files?
Radarr doesn’t delete video files unless replacing them with a new one, or commanded to delete them. It will delete related metadata files like images, subtitles, and nfo when it thinks a video file has been deleted though.
Your logs repeat with root folder ‘E:/Movies’ was not found while trying to import new media, but doesn’t mention anything else. Does that folder still exist, or was it also deleted? All your movies, or just some? Were other libraries modified? (tv shows)