The next time this happens, try this before restarting.
Go to the home screen and do a search. Put in the search box something that won't be in any file, like "zxc123zxc".
If the search box tells you that it is still indexing the new books, then you will know what is happening.
I seem to recall the last time the indexer came up here, that the only real option was to do what you have described, reboot the kindle to re-start the indexer.
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