Hello,
Devonthink was totally stuck with some kind of black screen and need to force quit.
Delete the app and instal does not change anything.
Then I had to delete the app using appcleaner I’ve lost :
Is there a way to recover those missing data in a backup file?
Why all those things not embedded in the data base???!!!
Are my 3000+ encoded files using personal meta data lost???
The preferences are stored in ~/Library/Preferences/com.devon-technologies.think3.plist, the metadata definition in ~/Library/Application Support/DEVONthink 3/CustomMetadata.plist. But this only the metadata definition, not the actual metadata of files which is stored in the databases. Where was your database located?
Finally, we discourage usage of apps like AppCleaner or CleanMyMac as they usually cause more harm than good.
I very thank you for this information!
Located in a directory called “database” which seems to pretty good synchronize thanks to iCloud
Im totally share your mind.
But Devonthink get strange behavior (firstly unable to drag and drop mail or mail attachement then unable the application got totally black screen and beed to force quit). Reinstall does not repair anything and I had to totally delete the app using AppCleaner. Sadly.
As advised by @cgrunenberg, as another voice, please avoid AppCleaner, at least for DEVONthink so as to not cause these problems. Trouble.
Reinstallation rarely fixes issues. But if you must (and maybe you did have to here, dunno), see page 6 (Ver 3.8.6 version of the PDF) of the outstanding “DEVONthink Handbook” where uninstalling is explained.
I agree it was a bad idea. Finally thanks to this problem I now know how to transfert this for my second Mac.
I would be really great to embed thos metadata and other setting directly inside the data base.
or I need to create something to backup this for next time I will refresh my Mac
KISS. Use Finder to copy the file(s) to somewhere safe. Or count on TimeMachine (or what you use for backup) when you refresh your Mac.
I guess you do a destructive “refresh”? Not something I do. Probably only once when Apple Care told me to do it and in the end not necessary. ¯\(ツ)/¯
You are right. Sometimes I do destructive refresh. Maybe a little too hard core 
Finally metadata and preferences are back inside the right directly.
One more thing :
I can’t find a rule I previsouly created. Where are they and what is the potential name for me to start a search?
Here are things I found I trash->
I searched this forum for “where are smart rules” and found a thread:
which should give you a clue about location of the file “SmartRules.plist”, which appears on your screen shot, so I guess you found it.
It seems to be what I’m looking for (retrieve in the trash), but I don’t know where to put It in the new hierarchy.
Edit : thanks for searching. When we have not so much time, afraid of possibly data lost, get tired and absolutely not knowledge in computer we can sometimes not find or even not starting to search this way.
Anyway it seems I’m not the first person finding it would be great to embed those data somewhere to not have to get your hand inside the beast copy/past this kind of files (which requires to show invisible items and so on)
When you chose to use AppCleaner or equiv, or do destructive refreshes, you need to be prepared to “get your hands inside the beast” to recover from such drastic action, IMHO.
Apple prescribes certain places where apps should put their config data. And I think apps should stick to that as a means to keep the stuff organized. Otherwise, no-one would know where to look for it anymore.
Situations where these data go missing are mostly related to using unnecessary tools (like “cleaners”) or “clean installs” and such. And possibly not having a proper backup.
“Embedding” these data somewhere else does obviously not help: The data just goes missing with the databases or wherever you’d want to embed it, not with the ~/Library/Application Support/DEVONthink 3 folder. Same same, but different.
Now I know.
But when you are no more able to use your application (strange black screen (probably because of Ventura)) , you use AppCleaner to be sure everything is cleaned.
But when you do that, you do not even know you can restore 3600 files / 4Gb of data in finger snap but 3 files lost somewhere will stuck you in the middle of nowhere. Thanks to this really good forum (And I want to thank everybody here for your help) I was able to find what / where files are and what they do.
When you are a end user, used to apple sync plug and play philosophy, you spent lot of time you do not always have to fond how to sort this.
anyway thank you all again
From the symptoms you’re describing, if this recurs, I would suspect deeper issues unrelated to DEVONthink.
That what I think too (not able to find what is the problem), but face to this sudden problem when you need to find files stuck in 4 database, you need to find something to be sure not everything is lost before revert back to a backup not necessarily up-to-date.
So I was able to revert files but some data were somewhere in the middle of some library / hierarchy you need to understand while you need to manage things etc etc
I’m not sure you are totally right.
I can :
if one day somebody broke, stole, or whatever happen to my computer I will have exactly the same pain. I will not use AppCleaner. I will be able to sync to my new computer my datebase with 3000+ files but thousand of metadata will missed > they will be stuck somewhere in deep hierarchy and will ask me time to find in help file, in this forum or somewhere else how to recover those tiny files.
That’s the reality. AppCleaner is visible part of the iceberg. Metadata embedded in my files is the big part and will be no more usable until I spend hour to understand what going on.
Sorry to be only end user
Reinstalling an app that confirms to Apple standards, if the system not restored using TimeMachine, requires a bit of care as you found out. It is not a simply related to syncing. What @chrillek wrote is correct. Probably should leave it at that.
Glad your seem to be back in business.
TY, yes everything back to normal. And moreover, now I know what files to backup in case I change my computer 
