Is this a known issue? I see there are some similar sounding questions on the forum from years ago. Most of the files contain PDF’s. Everything made it into Dropbox, why not DT?
Maybe aliases? DEVONthink skips Finder aliases.
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Turns out a lot of the PDF’s in the Dropbox folder on the mac are corrupted. Their cloud based equivalents are fine however so I downloaded them again, verified that were fine once downloaded and then attempted to copy them across to DT3. Up comes a logscreen with a litany of complaints - pretty much every file is ‘failed’. There are also a few ‘unknown formats’. I would like to have this stuff stored inside DT, if the only alternative is storing links to files which are nonetheless searchable by DT3 then I would be open to that - however- I do want my DT db’s encrypted (and their metadata) so is that a problem? I am intent on getting DT working but am obviously doing a lousy job cos this is as basic as it gets isn’t it? - moving files from one place to another. What am I missing? Back to the manual and all help appreciated.
Turns out a lot of the PDF’s in the Dropbox folder on the mac are corrupted.
I would be looking into why this occurred.
go on then give us a clue as to how you would do that 
Have you checked the health of the machine? File corruption isn’t a common thing and sometimes is a symptom of a hardware failure.
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Problem now solved and all folders and files sitting happily in DevonThink 3. It was nothing to do with DT, it was ‘Family Room’ within Dropbox that was the issue. As a result of your post I ran a diagnostic on my Mac for the first time and it came up clear. Thanks.
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Wonderful news - for you and us! 
Glad to hear it’s resolved and also that your diagnostics reported a healthy system!
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