Ryan Fuse in a different posting (see Do we DTP users really a need an outliner ?) mentioned indexing a folder of Scapple files, I did this and a really weird thing has just happened I do not know why, it probably is not a DevonThink problem but you never know! I had a folder in my Documents for Scapple stuff which had anything to do with Scapple and some 4 or 5 “Scapples”. I then indexed them in DevonThink ProOffice. On start up this morning the application Scapple had disappeared completely together with the contents of the folder in my Documents 
All my stuff was lost. Why this should happen I have no idea, very curious indeed. I have had to reinstall Scapple, but as I have back up I could retrieve the documents. Just thought I would heads up this in case it has happened to anyone else in indexing and really to record that it has happened for future reference.
You indexed a folder in Documents. And Scapple.app was installed in “Applications”. And they all disappeared? The only case where DEVONthink trashes indexed items is when you delete an indexed file inside DEVONthink, and then empty the Trash and select either “Files” or “Files and Folders” in this dialog:
Even if you had done that – it would still not trash Scapple.app unless you had also indexed Scapple.app, emptied the trash, and selected “Files”. (If you indexed anything in Applications, “Files and Folders” would have deleted all of your applications.)
Is any of that likely?
Thanks Korm for your posting. No absolutely none of that is possible as the only two things I did after indexing was (a) check that the indexed files appeared in DevonThink, which they did, and (b) shut down the computer for the night. I shall do the same thing again today and see whether or not the same happens when I open up tomorrow. I am inclined to think that it is my ageing laptop that is the problem but I have no idea why that should be the case. I shall report tomorrow!
Maybe also look at your laptop’s Trash to see if anything is there that should not be.
Or, just buy a new laptop 
Could you persuade my wife of its importance please Korm? 
Obviously – all of your fondest thoughts were memorialized in those regretfully lost Scapple documents. Which would not have been lost were it not for the antique laptop you’re forced to struggle with every day.
Absolutely, the trouble with that argument though is that she knows full well that I back up every day
Update: Everything opened and worked fine this morning.
lol, funny thread.
Anyway, i have yet to lose my scapple apps or files yet. And even if i lose them i have backups. I use time machine and backblaze.
Maybe get a backup, Allsop?
I do backup as you do with Time Machine, thought that was clear from my posts 