Thanks for you answer.
We played around a bit more since I asked the question. It turned out that setting the second parameter of remove method to Persist.MASTER did cause the problem.
We do not have a master in our configuration. A quick guess is therefore that the old Couchbase server version did not check if there is one before trying to delete the value.
However since we are not running in master-slave mode we set it to Persist.NONE. In our case this solves the issue.