When you set up your DEVONthink profile in ScanSnap Home, just clear the “Manage in ScanSnap Home” checkbox.
This worked for me in DTPO, but I have admittedly not yet tried to scan anything to DT3, so maybe things have changed.
well, Mr_V, this is me declaring my (totally IT-centric, platonic) love for you! Was that checkbox always there? It seems sort of obvious really - works a treat! Thanks for that, you’ve saved me a lot of work!
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Hahaha, I’m happy that it makes your life easier!
I have to admit that I don’t know whether that checkbox had always been there since the first version of ScanSnap Home. At first, Home always saved thumbnails for me and the fact simply didn’t bother me all that much. I only found that checkbox after some time using the app!
When you set up your DEVONthink profile in ScanSnap Home, just clear the “Manage in ScanSnap Home” checkbox.
I think this is a recent update. I have to test this out here, but that will be a good answer for people who have complained about DEVONthink not cleaning up the ScanSnap software’s files.
Thanks!
I have a similar problem, but it’s with the older ScanSnap Manager software (v 6.3L70). My ScanSnap is old, too (S510M).
Even though I have it set to Scan to DEVONThink 3, it still insists on saving a duplicate file in the ~/Pictures folder, which I then have to go back and delete manually. I can’t find a way to disable it ;-(
Any thoughts?
I think you may be right.
However, all is still not 100%. I’ve just noticed by chance that the documents I scanned recently are still in the ScanSnap Home folder! In the past, ScanSnap home collected metadata and thumbnails, but no actual documents remained. Now the opposite is true. 
That said, I’ve changed a couple of things on my computer recently:
- Update ScanSnap Home (twice)
- Started using DEVONthink 3 beta
- Unchecked the “Manage in ScanSnap Home” checkbox
I’d have to go back and vary these variables one at a time — as far as possible — to see what caused the change in behaviour.
Where is this checkbox? I couldn’t find it.
Thank you.
It is unchecked & greyed out for some reason on my Mac
Just want to ask a naive question. What are the additional value in integrating the Scansnap s/w with 3.0?
Can’t users just set the destination of Scansnap or any scanner to an index macOS folder, and let smart rule to take care of everything, such as OCR and import to different groups in 3.0. In fact, that what I’m doing now. I just user my printer to wirelessly scan to an index folder on my Mac, and let smart rules to do all the jobs for me.
@VictorGav: In the DT3 preferences you can set up what DT does when it receives a file from a scanner (the tab is probably called “OCR”, but I’m OOO, so I can’t check just now - will update this post if necessary). One of the things you can set here is what to do with the original document (in DT2 the checkbox is “move to trash”). In DT2 this reliably worked for me - wherever ScanSnap was saving to, the original file was deleted by DT following OCR. Because there is a bug in DT3b1 and OCR is not triggered when a file arrives from ScanSnap I could imagine that the second step - deleting the file - might not be triggered either (disclaimer: I know there is a bug when using ScanSnapHome, but don’t know if it applies to the ScanSnap Manager too). So: check whether you have the appropriate checkboxes ticked and if yes, waiting for DT3b2 might be the answer.
@Mr_V: I’m out on a limb, guessing here: ScanSnapHome (SSH) has always placed the scan in a folder, as set in the scanning preferences. Previously, SSH then passed the scan to DT2, which - if set up to do so - performed OCR and then moved the original file (which SSH had saved) to trash. Because of a bug in DT3b1 OCR is not automatically triggered even if appropriately set up; presumably the second step (move to trash) is also not triggered, which is why you are finding a copy of the document in the SSH folder.
ie: SSH always saves the file to the folder designated in the scan preferences. The “manage in SSH” checkbox only influences whether the file (and its thumbnail) is visible/managed in SSH. The file would usually be deleted by DT3 (even if the file is managed by SSH, actually, meaning that only the thumbnail [and possibly other copies of the file in temporary folders, library, wherever…] remains in SSH if DT is set up that way).
@Blanc I think we’re all guessing here. 
I’ll try to do a few tests this afternoon when I’m at home with my scanner again…
@Blanc is essentially correct on what the integration actually does. People mistakenly think it’s DEVONthink controlling the ScanSnap (which Fujitsu doesn’t allow). The integration was DEVONthink was aware of what and where the ScanSnap software was sending scans and would import - and optionally OCR - from that location.
And for any passers-by: That location should not be DEVONthink’s Global Inbox. Using the default location suggested by the ScanSnap software is generally advisable.
D’OH! Of course, there is indeed a “Move to Trash” option in Preferences under OCR > Original Document, and I had left it deselected.
I tried selecting the option, and now the document vanishes from the ScanSnap folder once DT3 has run OCR and filed the document away.
Thanks for pointing me in the right direction, Blanc!
Just tried to scan for the first time with beta2, and DEVONthink did not automatically ORC the document that ScanSnap Home sent it, even though that setting is checked in Preferences.
I realise this is still an area that is actively being worked on; I just wanted to give my feedback!
Please see my solution for this here, maybe it will work for you: DT3b2 not performing OCR automatically
Aha, the old “wiggle the switch back and forth a couple of times” solution! 
Thanks, I’ll give it a bash!
… and, it works! Thanks!
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Oooooh, is that the technical term? 