Doing “Verify & Repair” I get orphaned files located within the directory files.noindex and there e.g. pdf/1/ (opened in finder with “show package contents”)
I can move them to another directory, put them into DTPO inbox and check if they are duplicates, throw away or put them into the right place. so far so good.
but there is another directory “Orphans” which contains nearly 14.000 items. 
nearly as much as I have altogether in “real” DTPO
why/when does DTPO put them there? they do not appear within the DTPO window.
how do I proceed? - thanks.
That’s not normal, indicating that you have been having database damage.
Please send a message to Support, with the following information:
The number of documents and the total number of words in the database (from File > Database Properties).
A copy of a recent DEVONthink crash report, pasted into your message. If you are using Lion or Mountain Lion, go to the Finder. Click on your user account in the left column, then press Shift-Command-G. In the query field, type “~/Library” (without the quotation marks). Now your user Library is visible. Click on it, then on Logs, then on CrashReporter. If there’s a recent DEVONthink app crash report, double-click on it to open it, then click in it and press Command-A to copy it to the clipboard, then paste it into your message to Support.
will follow your hints
this will help the DT guys to improve the program but what shall I do with the 14.000 files?
import into DTPO, look if they are all duplicates, just delete the contents of “Orphans”? … or delete the directory?
“verify & repair” reports still 400 orphaned files within files.noindex, but I will handle them. the database seems to be ok so far, DTPO working perfect.
I made some mistakes in the beginning, importing, converting into readable PDFs, deleting … suspect the problems / orphaned files come from that time …
thanks, martin