I ran into the same issue trying to merge two small (200+ and 1100+ people) projects. I had the larger project open and was trying to merge "B" (the smaller) into "A" and got the error message. On a whim, I closed the project and opened the other and tried merging what was then "A" into "B" and it seemed to go fine. I can't explain it but you may wish to give it a try.