Solved! Go to Solution.
I spent several hours with this problem and I have found another work-around. Null geometry does not convert but the .geodatabase also doesn't like extremely complex polygons with multiple holes cut out of them.
There is also a bug in the "Share as runtime content" in ArcMap. When the analyze or output window appear during the export, they reduce the extent of the export. The trick is to zoom out further than the full extent and pan up so that none of your features are covered by the output/analyze window during export. Seems like an odd bug.
The best solution would be for ArcCatalog to support the .geodatabase extension just like it does other formats.
If anyone is looking at this post with a similar problem, I have discussed it with Esri Technical Support at the Dev Summit and confirmed that there is a bug that appears to be fixed in 10.4.
If any of the layers/tables you are exporting to Runtime Content has a GlobalID column, then the export may fail and/or result in an incomplete runtime geodatabase. The only workaround is to delete the GlobalID columns before exporting.
I have not yet confirmed that the export succeeds in 10.4 or any versions of ArcGIS Pro.