See the attached screen shot of the resolve conflicts screen. I have a few conflicts (which may have been created when moving and renaming folders) that are not file conflicts but folder conflicts. I am not under the impression that having two folders (autopopulating or otherwise) with the same name is a problem. In any case, these folders do not actually exist on the hard drive. They are apparently referenced in the list of VIs down below. Clicking "Use Selected Item" only appears to resolve the conflict, as after prompting for saving of the files, the newly resolved conflict diappears and then reappears right away at the bottom of the list.
It is true that these so-called conflicts are not directly causing any serious problems, but I have three now, instead of one, after a recent move of some files, and I do not wish to continue accumulating these conflicts.
I'm not sure if this is relevant, but we are using LabVIEW 8.x file paths in the executable.