I upgraded to 2.3 and copied all my files over. Most everything seems to be working (a few tweaks needed with my theme), that is except my categories. When I go to the Manage Category tab I have a set of categories that show up that are Parent categories but it is not the list from my previous version of WP and all the children are gone. All of my posts show their correct categories and when you click on them they go to the archives however in the categories panel in admin none of the categories are there.
If I add new category children to the parents it's going to change my links.
Would this completely mess up my structure?
Has anyone else experienced this type of problem and if so how did you resolve it.