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First off, sorry that you are running into trouble with this. We'll see if we can get things straightened out for you.
There are a couple of issues at work here, and I think they're combining to yield the results you are seeing.
1) Changing the location of the DAOS repository after there is data stored there is A Bad Thing To Do. Unless you are moving the existing data to the new location, or you are positive that there is no data remaining there, it should not be changed for any reason. Aside from that, I've seen situations where it takes *two* server restarts in order to pick up a change to the DAOS repository path. I'd suggest changing the path back to the location you were using originally, and then restarting Domino twice.
2) The daos.cfg file keeps track of how many NLO files are in each directory so DAOS knows what directory to add new files to. It sounds like your earlier experiments yielded 4 directories worth of NLO files. When you changed the base path of the DAOS repository, it was still using the old daos.cfg file, and started off at directory 0004. The daos.cfg file was designed to be expendable, and will be re-created on startup if necessary. I'd suggest stopping Domino, renaming daos.cfg to daos.cfg.bak, and then starting Domino again. This will create a new daos.cfg file that has file counts that are correct for the base path. (Note that you should complete step 1 above before doing this)
3) Although I am not aware of any incompatibilities, upgrading between B2 and release does look like it was the start of the problems. To address this, once you have completed 1 and 2 above, I'd suggest doing a DAOS resync. In your case, the DAOS catalog may still indicate it is properly synchronized, so forcing the resync is best. Issue the Domino console command "tell daosmgr resync force" to initiate the resync. This indexes all of the NLO files, and also counts all the references to them in all of your NSFs, so it may take some time to complete.
After that is done, try adding a new attachment and see if the original problem has been corrected.
Feedback response number PMAO7N85BV created by ~Dan Zeklulygon on 01/12/2009