Going to mark this one as resolved as have found out what is causing the issue.
/vol/filedir is a mount point to an S3 Bucket, which uses s3fs. This seemingly periodically drops the mount, thus loses the connection to dataroot. This I have discovered is a legacy setup, so will update this to not use S3 in the future, but have used this watchdog script to remount the path if it detects it has dropped out. Not ideal, but ensures it doesn't stay out of service for now.