Glad to see you figured it out so quickly.
I just thought I'd add, for future reference that I used Unison for awhile..and found it 'ok' to get your feet wet in learning about Rsync..
After a lot of frustration with Unison.. it's lack of features, overwhelming use of terms that NOONE has a clue to what they EXACTLY mean, and the fact that it is not supported anymore (I think).. I just took the time to learn about using Rsync alone.
It's manual is cleaner and more easily understood... even tho it is basically the same otherwise as Rsyncs.
For instance, with the issue you were having.. the adding of the --delete switch would have been the cause of your problems.. however, (I think) that the ONLY way you could have REMOVED this switch from UNISON, would be to run it from the command line... which, at this point, you might as well do away with all the fluff & guff.. and go straight to using Rsync.
Anyways.. good luck in the future with your work & projects