Thank you for your post.
Error 10002 is a Disk Full message. Make sure the drive is not in fact full. Server logs can continue to grow in size, so check the size of the FileMaker Server logs.
KB 6551 will provide the relevant information pertaining to locating the log files.
If the logs are large in size, then remove the files and try again.
The STOP command is sufficient to properly close the hosted database files. The log files should show "Stopping FIleMaker Server..." followed by "Stopping FileMaker Database Engine..." followed by the closing of each database file, followed by a confirmation each database is closed, followed by the final confirmations that the "FileMaker Database Engine stopped" and "FileMaker Server stopped."