Hi Thomas,
it's little bit time from posting your problem, but if there's anybody with same issue, i decided to post solution that works fine for me.
Program: Arc gis pro 2.4.
Problem: After calculating geometry in shapefile column, there wasn't any way to repeat calculation after editing area of shapes or merging them. Program gives me the message, that "Input feature class is not registered as versioned. Failed to execute (CalculateGeometryAttributes)."
Solution:
1) Close the application and open it again. Close browsers that can use the edited file (windows explorer, etc.)
2) Remove column with calculated geometry.
3) If the program don't remove column from table visually, but in shapefile it is deleted - remove layer from layout and add it again. (Refreshing doesn't worked for me.)
4) Create new column and calculate geometry again. (After finish editing you would like.)
I thing it can be solved by creating new column for calculation without erasing the old one, but i want just one column with shape geometry in my shapefile.
Don't know, why the problem is there, but hope, that in newer wersions of Pro it's solved.
Best regards
Dominik