I'm back with the same set of issues.
Twice in the past week, I have tried to merge where the "source" and "workstation" versions were not in conflict and both times, after the merge had been generated, I got error messages that prevented me from comitting them. The first time, I got an error that my merge had to include the link - even though I had the link selected. The second time, I got an error that a file was duplicated, if I try to uncheck the file, I get an error that I have to process all the files in the merge. Undoing everything in the merge really is not an option for me. I will probably end up manually copying the files out of the project, "undoing" and then copying them back in.