I’m reviewing PDFs and highlighting them in DEVONthink Pro Office. They’re indexed files. The files are open over the course of hours (it’s dense reading, okay?).
When I check the file directories in DEVONthink and Finder, I’m discovering copies of the files that I haven’t created. The copies include some of the highlights I’ve added to the PDF.
It seems like the “genuine” file is the latest and greatest—i.e., it has all of the annotations—while I don’t think the copies are exact duplicates (e.g., they seem to be being created as I move through the document over time).
If you are worried about data loss as a result of changing your preferences (looks like you are also doing academic reading and don’t particularly fancy reading a paper twice), my anecdotal experience is that I have seen a significant decrease of this happening since switching from WebDAV to iCloud. However, I must admit I had far fewer occurrences of this to begin with.
It’s always interesting to learn about different experiences. I’m using WebDAV as my sync engine since a long time and never experienced any duplicates.