Don't know which version you are running, but it might be worth a try.
I remember an ugly bug the prevented snippets, chunks, templates and plugins from being displayed if they were stored inside a category which was nested inside another category that had no content except other categories.
Example:
Category1
|--Chunk1
|--Chunk2
|--Category1.1
|--Category1.1.1
|--Chunk3 You CAN'T see that one, because Category1.1 is empty except for another Category.
|--Category1.2
|--Chunk4
|--Category1.2.1
|--Chunk5 You CAN see that one, because inside Category1.2 is another chunk (Chunk4)
Its easy to make them appear again. Add some Dummy Content to the empty category and all missing elements in the children category show up again. Move all templates from that category so they fit into the rule I described above.