Yes you can pause clean index. You can do it also on Advanced settings -> Maintenance -> I -> item 0.
Clean index only looks for every word/album and word/photo entry if the word still appears in the album or photo, otherwise the album / photo id is erased from the index entry. Unused entries (where no album and no photo ids are in) are removed at the end of the cleanup process.
On Basic settings -> Search -> I -> Item 35, you can list the actual index table, and see if there is something wrong.
You should know that there is an important difference between the interactive and the background way of re-indexing.
The interactive way clears the index. When running the album re-index, all album ids are removed from the index table, when running the photo re-index, all photo ids are removed form the index table. A said before, completely empty entried will be removed at the end of the cleanup proc.
When running the background process, the table will not be cleared up front, because this proc may take substantial time and we do not want missing entries for a long time.
If your index is a mess and you want ‘start all over’, run the remake proc interactively (using the Start! button AND KEEP THE BROWSER TAB OPEN until completion, otherwise you will have to restart later and in the mean time your index is incomplete. Run them both, but not at the same time!