I worked with Novell Netware 5.0 until earlier this year. Occasionally, similar issues would arise. I finally concluded that somehow some links were never dropped even though the table was not in use anymore. Sometimes this happened when the user locked up (or thought they had) and rebooted. Since we still use some dBase 5.0 DOS programs, here's what I would do, where each step would get more agressive until the problem was resolved. Though I don't have a specific answer for you, I hope something here may help...
1. Close the DOS window then try again.
2. Log off and back on then try again.
3. Shut down and reboot or restart the offending workstation then try again. (Just once I had a user "turn off" his workstation and it locked up his open files until it was turned on AND logged on. Apparently the old links weren't cleared until the new user's logon forced the removal of the old connection, so possibly the next point would have had the same effect as a reboot/logon.)
4. At the server station (or in a remote control window) CLEAR the offending workstation's connection. First lookup the user's connection number. As I recall, on our system the users had 2 connection numbers, but only one held the links to files. Then at the CLI type: CLEAR STATION {number}
5. Give up and reboot the server. (Generally if we got to this point it was because the server was "thrashing" with constant disk access and nothing fixed that. Most other issues were cleared up by point 4. We never did figure out a satisfactory reason or solution for the thrashing though some posts indicated we should have had some sort of disk caching turned off.)
If a user calls me to report a problem, I generally start with step 3 and tell them to reboot and log back in. It isn't worth the effort to tell them a long series of steps.
For your specific problem, I'd suggest clearing the workstaion from the server (step 4) and see if that doesn't do it.
By the way, Win2000 Server also gets weird issues too now and again, and every once in a while it has to be rebooted in the middle of the day, so no server is totally invulnerable.
If possible I'd suggest a server reboot periodically such as once every 2 to 3 weeks as preventative maintenance to "clean up" any leftover links and other invisible odds and ends. Better to do it planned during a quiet time rather than in the middle of a busy day! Hey, these days you have to do that anyway, at least for Microsoft systems, just to install security patches!
Hmm, new licenses are expensive, I wonder what the market is for spare Netware 5.0 licenses...