[ifoner]

The first step is a better message. The second step is making sure it doesn't happen more often than it should.

I'd put them in this order because the first problem (I'm a new OF user) is understanding the question, and it's a scary question to begin with. The fear is that if you answer incorrectly you might lose data.

If I understood the message, I'd be less bothered that it happened unexpectedly.

Why don't we toss in some suggestions for messages. To start, I'd say that the term 'database' is ambiguous since the average user buying OF doesn't think they are buying a database. Also, it's not just a database (in the background) that is going to restart.

I'll throw out one to start.
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"Recent sync has updated your data. OmniFocus needs to restart"

- then buttons that make sense in this context.