I tried to look this up on the DEVONthink forum but could not spot a simple answer
I have a folder containing pdf files, I use Hazel to move newly download pdf files to this folder. I created a new database in DT3 and use indexing to store the pdf file details. My question is - do I have to re-index the folder regularly to include the newly added pdf files?
No, DT should automatically find and display those new PDFs.
Not if you index the folder. It should pick up any changes.
See page 53
https://download.devontechnologies.com/download/devonthink/3.8.6/DEVONthink%20Manual.pdf#page52
thank you both, I am clear now
While indexing is a valid method to use DT3, you are aware of the possible Backsides of indexing vs. importing your files, right!?
Is there a way to “re-index” a folder without removing and re-adding. When I try to index my obsidian folder I have issues. It uses iCloud, and I keep DT running in my Mac. Often times I access on my iPhone obsidian and then it won’t pic up those files on devonthink since they may not automatically download from iCloud. Occasionally have had to remove and re-add the indexed files and would be better if I could somehow have it “re-scan.”
Pick the index group, then Menu: File → Update Items.
Make sure you have “Optimise Mac Storage” off for the applicable folders so that DEVONthink can find them. DEVONthink won’t reach out to files that are offloaded by Apple’s iCloud.
Indexing fully described in the DEVONthink Manual. If you’ve not yet read it, recommend you do.
I can only imagine the DEVONthink programmers tearing their hair over this use case. Keeping synced across devices with files being added by another app besides DEVONthink itself … this is a really hard thing to do. It is amazing to me that it works at all. 
Thanks exactly what I was looking for!
Excellent. Be sure to read about and understand Indexing in the DEVONthink Manual.
Keeping files in sync across devices appears to work sometimes but doing it fast enough and consistently enough to keep users happy is the hard part. It helps to provide a manual operation that users can perform themselves to try to force syncing.
I have. Devonthink markdown editor is horrible and nearly unusable for mobile, but it is nice to be able to have everything searched from single location. And I like ability for DTP to make summary highlights and annotation files, but they must maintain in the database. If I move to obsidian then DTP will make a new file when exporting or adding annotation text.
When I index just one folder of obsidian into that database I do get best of both worlds (file remains linked to source document, and can be edited either place). But yes the sync with indexing (since on iCloud) has been a mess to say the least.
You can use whatever Markdown or text editor you want. Use “Open With…” and to make default change the macOS default per Apple’s documentation https://support.apple.com/en-gb/guide/mac-help/mh35597/mac No need to be stuck with something you find “horrible”.
Using iCloud for syching is probably not going to work at all if you set Apple’s iCloud to “Optimise Mac Storage” to the “on” as it deletes files to “help” you.
There are better ways to sync. See the DEVONthink Manual.
While this workflow is fine on macOS, my workflow is predominantly iOS. This doesn’t work well on iOS at all unfortunately.
Edited: spelling
Depending on your Markdown Editor of choice, you could also open the DTP Files direct from the Editor, without the detour via DTP.
Further to @ulli’s comment, I sometimes use ByWord to edit on iOS devices text/md files in DEVONthink ToGo. Textastic also can do it. Gives me plenty of flexibility so I can focus on the writing and not the technology. Probably can do same with other editors that you don’t find horrible.
That’s a fair point. I should clarify, I am using obsidian as my text editor and have no plans to move from that. I have a reasonable workflow that is ok. (Once Apple notes gets templates, some more advanced sorting, and iOS allows colors for text to progressively summarize) I will probably move back however).
I dream of using devonthink for everything, but it’s not great as an editor in my subjective opinion. Also, devonthink to go is no where near as full features as it’s max counterpart. For now I’m sticking with obsidian as text and devonthink essentially as a local Evernote. (And even this is only because I feel obligated due to the money spent, once synology ds drive adds better tag search to include Boolean I think I’m out of DT).
TLDR: using obsidian and DT only
Obsidian seems to be one of the few Apps, that seems to be not able to get direct access towards the DTP Files, but as far as I understand Obsidian is also not considering itself as a “Markdown-Editor”.
And, my understanding is that Obsidian has their own version of “standard” Markdown …
(As if this sort of forking has never happened before in the history of Computing Technology 
)
I think I know but I have re-reading the manual just to be sure, and there is nothing to lose in my case, all my pdf files would be still there, worst I can restart creating the DT3 database again