Sorry for late reply. Custom CSS code is stored as a Theme Option value in WordPress database options table.
If you did not accidentally deleted it, then maybe your server timed out while saving the Theme Option values.
You can use firefox firebug extension to see if your saving process is complete.
You can also check your error logs to see if you encounter any memory limit or any type of server related error.
Sorry, I do not have a specify answer to this issue.
I suggest for your future development, you could save a copy of your custom css code in a text file using your desktop text editor, doing this will ensure that you have a safe backup.