I have had this issue happen a few times to me with no real fixes appearing in google. So I did some trouble shooting on my own and have figured out the problem.
It is a MySQL issue and they way for your categories and tags to reappear in your web admin (wp-admin) section is to restart MySQL.
I have a VPS so I logged onto my control panel section and restarted the service and the issue was fixed!
If you are on a shared hosting plan you might have to call or email your provider and ask them to restart MySQL.
I do not know any other fix but this restart of service fixed my issue of missing tags and categories.