Why exclude folder from Dropbox when doing Dropbox sync??

The instructions for sync via Dropbox also say:

Note: If you are using Dropbox and the Dropbox app, it is advisable to exclude the "DEVONthink" folder inside the "Apps" folder from being synchronized with your Mac. This keeps the Dropbox app from wasting valuable disk space re-downloading all changes you've made to your databases, and from spamming you with notifications.

I don’t understand: isn’t the whole point of using Dropbox so that the same info is available on multiple machines - how is DevonThink going to sync anything if Dropbox is ignoring its data and not copying it to client machines?

Probably because DT doesn’t sync through the Dropbox folder you see on your Mac but directly to Dropbox via their API.

(but I’m just guessing based on that I have a separate Dropbox account for the syncing and it’s not used for anything else and thus is not available as folder on any machine I have)

@jem stated it correctly. The Dropbox API that DEVONthink sync uses does not require you to sync the DEVONthink folder inside the Dropbox “Apps” folder to your desktop. The data are synced to Dropbox’s servers, which is sufficient. The Apps folder is only used for developers who use the Dropbox API. (See Dropbox’s developer help.)

BTW, @mleven77 did not include the entire quote from DEVONthink > Help. The entire selection is helpful in context:

Somehow I missed this tip. DTPO was syncing my entire database to Dropbox even tho I had replicated only three folders into the Mobile Sync. I ran out of space when I only wanted to sync 300 mB of data. Deleted the DTPO folder in the Apps folder and tried again. Linked everything every time. Now I’ve deselected the DPTO folder, per your instructions. Am re-syncing now. Hopefully it will work. Will advise.

You are going to run into problems again. DEVONthink Syncs the entire database via Preferences > Sync. The Mobile Sync folder is only for use with DEVONthink To Go. You cannot selectively Sync part of a DEVONthink database to Dropbox. The only way to do what you’re trying to do is to create a smaller database just for Syncing.