To help @blanc (and I’ll pitch in) with others, a bit more clarification is needed.
: what makes you conclude the databases are “corrupted”? are you calling missing files “corruption”? What are symptoms you notice for “corruption”?
: can you clarify “upon further inspection, those files did still exist in their proper places within the databse, so I’m not sure where they came from”… You say this is past tense. So is this state no longer the case? What is the current state? Once imported DEVONthink doesn’t remember where files came from (far as I know, and if it does it’s irrelevant since I normally delete important files at their source), so you have to figure out if the “came from” location is valid, or the DEVONthink version is valid as the “current and good” version.
: You mention were DEVONthink (DT) is installed on “system” volume. The normal place for the application to be installed in “Macintosh HD/Applications”. Is it not there? If not there, a reason for why you installed differently? Why do you think this is relevant to the problem?
: What version of DEVONthink do you use? 3.6.1 is the current version.
: You say all files are imported, but not indexed in place. “Missing Files” sometimes happens with indexed files when the file does indeed go “missing”, e.g. it is not where DEVONthink last saw the file. DEVONthink doesn’t go hunting for missing files. What makes you believe the files ar “missing” and are you sure they are not at indexed locations?
: Are there any other computers involved? Where else do you have DEVONthink or DEVONthink ToGo (the IOS app) installed and running? and if so what versions. Do they also see “missing” corruption?
: If you are seeing file corruption (or is is just “missing files”), that could be occurring on either or all of your machines running DEVONthink, and could have nothing to do with DEVONthink. Have you used the OSX “Disk Utility” to do a repair on your hard disks(?) to make sure all is well? That should fix file/folder/disk corruption (but not the “missing file” problem, if that the problem).
: Since you didn’t mention other computers, my hunch is that maybe only one is involved? If this is true, then why have sync? Or maybe you do have other machines involved, and then sync is appropriate. But having two “cloud” sync locations doens’t help matters, especially when you say you were unhappy with Apple iCloud. (before suggesting changes, I’d for sure recommend you “clean” the iCloud sync location to stop using it on all devices.)
: Why is Time Machine NOT backing up “Application Support/DevonThink 3”? Did you exclude it in TimeMachine? If so, why? Is this folder actually “/Users/YOURUSERID/Library/Application Support”? Why do you think this backup exclusion is relevant? Is TimeMachine backing up the folder(s) where the databases are?
: I am confused about where your database files (actually “packages”) are located. Could you please give the full path names of each of your databases please (including file name and file extensions) DEVONthink menu: File/Database Properties …, top of the info window.
: I’m curious why you have encrypted the DEVONthink databases? That of course is your choice and depends on the sensitivity of the information. I get that. But to protect against what? Is you computer not sufficiently secure again someone else getting physical access to the machine with your ID? Are you using Apple’s FileVault on your computer(s) encrypt the data on your disk? If so, then is double encryption worth it to you? Just asking.