Hi there,
don’t worry, it’s a weird Christmas and having converted 25,000 files in the past few days has maybe left me a bit irk-able. 
I guess my problem is that I am expecting somebody to tell me that “this is not the way you should work with DevonThink” while it is the way that I work and want to work.
The files are stored externally on a harddisk, I am not even attempting to use cloud services, with terrabytes of data that would just be too much.
I work with them not through DevonThink but through Finder, Word, XMind, Dramatica etc.
So there are essentially two things happening to them outside of DevonThink:
- I edit them / and create new items (which requires an update of the DevonThink database)
And then there are the things that I have done in the past days, I have converted 25,000 doc files into docx files so they survive and I can still read them while Word has already decided that it cannot read its own format anymore. In doing so, I created new files and
- deleted the other files from the hard disk and from trash.
All of this sometimes has to be done outside of DevonThink because the workflow demands it or sometimes I just do it for no apparent reason at all. 
Both cases leave me with a database that has missing files:
- the new files and the edited files aren’t updated (as DevonThink is not constantly running in the background checking on changed files, I assume.)
- the deleted files are shown as missing and also listed on updating the index that they are missing, which is correct.
Now I want to stop short of creating databases every week, as I have just done. With 25,000 file changes I didn’t mind to let the computer run over night to let DevonThink create and thus update its database. However, this is a time consuming process and I am looking for a way to make that easier.
How can I ask DevonThink to update the edited and new files that have been created after the initial database was created.
And How can I ask DevonThink to update and remove the entries of the files that have been removed physically as well.
I do presume these are two tasks and I have found a rather volatile forum entry about that which has left me curious about the question if there is something that I am missing without somebody telling me that I’m doing it wrong. 
Alex.