Indexed document suddenly shows in non-existing folder! I'm worried!

The webserver is an internal component of DEVONthink Server so our app needs to be running. Just mentioning it.

I’ve had mixed experiences with Dropbox and iCloud (independent of DT), mixed ones with DT indexing files in Dropbox, and mixed ones with external drives. At the moment, I am indexing files on my computer’s hard drive and indexing others in Dropbox, and I am backing up in external drives with manual and automatic backups, but I am not satisfied with my current situation.

By “mixed” I mean some files not syncing properly and some data corrupted in Dropbox (PPT, in particular, seems touchy). iCloud has been unavailable or surprisingly slow to sync at times. When I index files in Dropbox with DT, I’ve had some unexplained sync conflicts that produce copies of the problematic files. For some reason, in the last few months, I have had several external drives fail on me. Fortunately, in all cases, I had backups, and nothing was permanently lost or corrupted, but there was at least one time when I was down to a single backup standing between me and issues.

Advice based on my experience:
(1) I don’t know if DT was ever to blame for any of the issues I have faced, and DT tends to work really smoothly with 28,000+ items and over 230GB in my current database (that’s pretty impressive if you compare it to competitors), but a kind of general rule of thumb I have is to try not to do too many massive changes at once (like reorganizing all of my files), because this has led to issues in the past.
(2) As for the cloud, I generally avoid keeping anything sensitive or important on it because stuff happens. DT is the exception, but all of that is encrypted.
(3) I appear to have removed a lot of friction by just using a single computer (the more I synced, the more problems I seemed to have with sync conflicts, orphaned files, and other oddities). All of the issues could well be user errors, but I just don’t have as many problems when I keep things simple.
(3) As much as I would like to work more, or even primarily with iOS (I have done so in the past), this generally doesn’t end well – iOS apps are insufficient for the tasks I throw at them, the devices have frozen up on me and lost data in the past, I am almost never completely in sync, and I tend to be less efficient overall (things can be done on iOS, but they often ought to be done on OSX).
(4) Whenever possible, I work with txt files. Again and again, I’ve found that the more complexity beyond text files that I add, the less enjoyable it is in the long-run. I have even been burned with markdown files in the past. In particular, a lot of the work I have done over the last three years has been in text files.

It might seem odd to give advice after admitting that I am not even satisfied with the workflow I have, but most of my advice is about avoiding complexity–it seems to roughly track with what others have said about their cloud experiences and so forth. In other words, I may not have my workflow where I want it to be yet, but I at least know some of the things I don’t want to be doing.

I’d be open to any advice about how to improve my workflow, but with so much data (3 terabytes or so on external drives and my computer being nearly full with “working” files on its drive), I suppose I am an edge case of sorts. At some point, I am hoping to move away from cloud services as much as possible and try to reduce my “working” DT database to a handful of GBs–the bottleneck seems to be that I don’t use all of my files all the time, but I use a lot of them some of the time.

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Amen

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