iMessage (iOS 10) doesn't index messages properly Here's the situation. I backed up an old iPhone 5S to iTunes on Windows via a  USB cable. I bought a new iPhone SE and restored the backup onto it. Everything works fine...except...no past messages show in Messages. The view, that usually shows them in reverse chronological order, is empty. Using the search widget doesn't find anything either. However, after creating a new message, that goes to one of the existing contacts, suddenly all the past messages appear in the chain!

Obviously the messages are on the device, but not indexed properly, probably a result of the backup and restore. Is there some way to re-index them so they'll show in the chronological view and be searchable via the search widget? Would another backup and restore help?

Seems to be related to Weeks after updating to iOS 10.0.1, all but ~5 most recent messages disappeared, and messages would no longer organize by time and Old iMessages and text messages have all disappeared after iOS 10 update? neither of which got an answer.
According to Apple's engineering department, backups only store the past 200 messages in the search database. The rest are stored for regular viewing, just not in the database.

"What the customer is experiencing is actually considered expected behavior.  With the release of iOS 10, customers are now only able to search the last 200 messages with Spotlight or the in-app search. This would include the last 200 sent and received messages.

The 200 searchable messages limit is only after restoring from a backup prior to iOS 10.  This is why devices that had the same Messages database and were not restored from a backup when they upgraded to iOS 10 can still search prior to the 200 limit.

If the customer would like to see this function in a different manner going forward, please encourage the customer to submit feedback at apple.com/feedback. “