On the filesystem I have some zero byte files. As stated years ago DEVONthink complains than.
But back then the fabulous cgrunenberg mentioned “The next release will improve this.”
So now, thankfully a few great releases later my question is: How can I now tell DEVONthink to accept zero byte files (and with this get rid of the repeated “Failed database verification” errors)?
Just curious. Why do you want zero byte files in DEVONthink? DEVONthink specialises on finding stuff in files, and if there is nothing in the files what is the point?
Perhaps as a work-around make those files with one character (a space?) in them or something until something changes in DEVONthink.
Thanks for chiming in @rmschne!
Well, I don’t want them necessarily in DEVONthink, but they are part of the directory tree I index with DEVONthink.
Certainly a good workaround for most situations. However some files are again and again auto-generated on the filesystem by other tools. (E.g. LaTeX creates zero-byte *.snm files which I don’t want to be forced to delete just for DEVONthink not to complain.)
I’m just hoping that DEVONthink now offers a mechanism to deal with these files! 
Oh, I now get the issue you experience. I don’t ever see this with my LaTeX folders as I only put the compiled document (even if a draft) resulting from my writings into DEVONthink. Never felt the need to do much work in DEVONthink through the whole LaTeX folder/file structure. I try to avoid cluttering up DEVONthink with unneeded stuff–but being the packrat that I am, it’s difficult. If I had need to search a LaTeX project files I’d use a search tool (Spotlight, EasyFind, or something else).