Thank you calbzam.
I did some further investigation.
Checking the Deleted Section in Pending Changes actually pushed the process.
To my opinion, the files shown had nothing to do with deleted files (they remaining files were added only on the source side, so an automatic merge would was expected for those files). But somehow checking the deleted checkbox triggered the Process All merges in a way it completed normally.
The merge was ok as was the final result set.
So the problem is solved although I can not explain why it was stuck.
Thanks for your contribution!