A word of warning: I had a similar situation and I think I might have set a new world record: it took a new Kindle THREE DAYS AND NIGHTS to finish indexing 1,800 (.mobi, non-DRM) books dumped on it all at once (because I was doing it for someone else and had no other option).
So if you do go this route, be sure to simply keep the thing plugged in while the indexing is going on or it will quickly zap your battery.
To find out when or whether indexing has been completed, type a nonsense string (e.g. dheywrsoithewrw) at the Home screen and press Enter, then wait for quite some time. If indexing is still underway the result will be a screen telling you how many books are still left to index.
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