You cannot influence the indexing process. As soon as you put a book on the Kindle, the device starts indexing it. And if you put 1000 books on the Kindle, it will start indexing 1000 books...
About the rest of your post, I can only guess what you were trying to say.
- Yes, it's enough to replace CollectionsManager.azw2
- No, the previous version was not "corrupted". But the new one has more error checks and tries to prevent a few of the problems which you previously reported (and which were not expected to occur).