I tested something that I know is risky, and it seems to work fine. I have a 10,000 item library of EF documents, and I wanted to Index some folders from EF in Devonthink Pro. That works fine. The next step is that DTP shows file names, and does not show Titles. (At least, not that I can figure out.) So I tried manually changing the file names in DTP.
The result is to create an apparent new file back in EagleFiler, with the new name. The old file in EF gets a file size of 0 bytes. (I have to run Scan For New Files to see the renamed files.) This appears to work just fine. Editing the file using DTP actually edits them in their original (EF) directory, so the changes show up in both programs. Then in EF I delete (move to trash) the files with a size of 0 bytes.
Is there any problem with this procedure? If it is safe, it will enable me to use both programs on the same set of files. However I will have to be careful about moving indexed files in DTP; I’m not sure what that would do back in their actual homes.