Indexing exported files error

after exporting nearly 50.000 files from my database and indexing them into a new database, they disappear if I erase the old db. When I check the files in the finder, they are really there (I can open them with the original application (e.g. Acrobat or MS Word). Checking the path to the files all seems correct. I am using Devonthink Pro Office 2.0pb2 under Mac OS 10.5.8.
Any suggestions? Thanks for help!

Remove all DEVONtech_storage files inside the exported folders and index them again or wait for the next public beta.