Today we heard the result from Oracle Tech Support:
“This is the expected behavior when you load #Missing cells through Excel Add-In or SmartView into an ASO application. The load operations through Excel Add-In loads data into an incremental slice using override mode. In this mode when you load #Missing values into cells that already have a non-missing value, they will be replaced with 0 values.“
Not many companies are writing back to ASO at this time and I wasn't yet aware of this behavior, but now we now another one of the limitations of ASO writeback.