Encrypting sync stores and encryption in general:

I set up DT database on a Mac and DT client on my iPhone. I don’t remember if I chose to encrypt the sync store. How do I find out if I did or not, and if not, can I add encryption now or need to start over?

Also, “Encrypted Databases” - how does that work? I saw it mentioned at DEVONtechnologies | How to Keep Your Data Private - once I use Disk Utility to create an encrypted file, then what?

How do I find out if I did or not, and if not, can I add encryption now or need to start over?

There is a property icon next to the sync store in DEVONthink’s Preferences > Sync and is shown in the illustration in the blog post you referred to.

No, you can’t just add encryption. This is covered in the In & Out > Sync > Basics and How To section of the built-in Help and manual

once I use Disk Utility to create an encrypted file, then what?

You don’t need to use Disk Utility for this purpose as DEVONthink can make its own encrypted databases. See Getting Started > Building Your Database in the manual or Help >Tutorials > Use Encryption.

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The property icon is a little key symbol, right - on the server side (DT3 running on my Mac), and if it’s there, it’s encrypted?

The key indicates an encryption key has been set, regardless if it’s a local or remote sync method.