If you're moving a folder to another directory where that folder already exists, and there are 'identical' files contained in the target folder... then the source folder will not be removed (which is what is being attempted when the error appears) because there are files left over (the ones you've 'skipped').
Otherwise, the stuff unique to the source HAS been moved the way you wanted... the only that hasn't happened is the remaining stuff from the SOURCE has not been deleted.
But, seeing as how the intent is to 'remove' the source files without also requiring unecessary time and disk activity to 'move' files from the source that already exist in the destination (and you don't want to have to go back and manually delete the remaining source data), then I suppose it's worth it to submit a feature request to GPSoft to add something like skipidentical and delsourceonmove options to the Copy WHENEXISTS argument... and maybe request that they intelligently delete the source files when a MOVE operation has been performed and the user has selected any of the skip options... maybe there's a 'reason' this is isn't already the case that I'm not aware of.
Thanks for the clarification, I had noticed that the missing files had in fact been copied.
I have been using a Picture manager called Firehand Ember (discontinued and no longer supported) which handles this situation gracefully, copy/moving missing files, and deleting the remaining files in the source.
So I admit I was "pushing the envelope" a bit to see if DOpus would handle it.
I have played a bit with the synchronise, with varying degrees of success. Need to work on that a bit more.