A few things:
Turning off iCloud Drive will have affected DEVONthink’s ability to sync; seeing as the iMac has its own local copy of the databases though, this should not lead to any loss of data. Reconnecting iCloud Drive should reenable sync, but should not lead to any data loss. Data loss could in theory occur when disconnection iCloud Drive if you were indexing from there, and started up DT at a point in time when iCloud Drive was not yet providing a local image of the files indexed. However, you state you are indexing files in Dropbox.
I think the following has happened:
- on the iMac, the files which were being referenced from Dropbox are no longer available in the local location they previously were, and have therefore been removed from the database.
- that change has not synced to the MBP (yet; presumably because iCloud Drive wasn’t available)
There can be a couple of reasons for the files no longer being available locally: One is a change to how Dropbox, OneDrive etc. work - see this thread. What is surprising to me, however, is the point in time at which this has happened - the pertinent updates to Dropbox have been around for a while. So I may be barking up the wrong tree - it would be worth taking a look at the thread though, and seeing whether you can relate anything to your situation.
Other reasons: when you turned off iCloud Drive, did you possibly opt to keep files on your Mac, possibly decreasing the amount of space available and triggering Dropbox to remove files from the local store? Is Dropbox set to keep the indexed files available locally at all times?
Where, exactly?