Unfortunately, we could not find a solution. After a couple of weeks the problem disappeared by itself and everything worked fine since then... until last week, when the problem appeared again. We have done NO changes in our QV files in the meanwhile. Maybe it is something in LN databases or server settings... no idea. The same files reload fine on another server, which is also very strange. I have no further ideas for now.
I know it is a long time since this question was posted but in case anyone else has a similar issue...
We found that the connections between Lotus Notes and Qlikview were not being automatically ended in the Task Manager so we tried putting in a Disconnect; statement between the end of each connection to Lotus notes and the next connection to Lotus Notes.
We used the same thing to resolve an issue with a connection to JDE. I don't know why it is not disconnecting automatically when it is reloading from the management console unfortunately, just how to fix it
For 99% of our cases that seemed to resolve the issue.