Dear Rick,
Unfortunately the most clueful people are now busy in meetings for the IDR project over the next couple of days: it is an unusually busy time for the OME team. We will make sure that somebody helps you this week, but we certainly regret the delay.
In the meantime, all I can suggest is to check your logs again and if you see some difference from before then go ahead and send us a new set. And, of course, if our delay in helping is too great, I'd alternatively suggest restoring from a backup taken before the problem started.
To make sure I am clear on this:
1. Your OMERO server ran into the system open-files limit during a large import.
2. No further imports could be made.
3. You increased the open-files limit substantially.
4. Despite restarts, deleting duplicate repositories, etc., your OMERO server is not recovering ability to accept further imports.
I wonder if anybody else in the community has run into the same issue of having to recover from this circumstance?
Cheers,
Mark