If you delete the files from the index folder they should come back after rebuilding the index.
When the index is rebuilt you should see messages logged in the log indicating that the index builders are indexing content. They write first to the mp_IndexingQueue table and then a task processes those rows into the index files.
If for some reason you are missing files in the /Setup/ProviderConfig/indexbuilders folder that could explain why indexing is not happening.
Hope it helps,
Joe