I have a counter which uses the Place Marker and Replace Marker traits. Each such marker was defined directly within the Place Marker or Replace Marker trait. Once these traits are actioned, the original counter is deleted (by the Delete trait). Now, when a Refresh Counters is performed every one of the new markers gets replaced by a copy of the original counter.
I found a workaround - instead of using the Define Marker functionality, I defined the markers as separate pieces in a Palette, and selected each of them from the Place Marker / Replace Marker traits. Now when a Refresh Counters is performed, each of the newly placed markers remains in place.