by Emma Richardson.
You have give us very little information - Moodle version, exact process.
When you delete a category in 3.0, you have to actually select to delete the courses in the category - are you sure that you deleted them? Are you sure that they are not just in another category now?
If you do not have a backup of your courses or your site, then you are in trouble...unless someone has some magical trick to rebuild them, I would think they are lost.