We have build a mobile app (I am working in the windows version currently) that uses SQLite geodatabase files for rendering at closer zoom scales, and VTPK files farther out. These are generated via ArcGIS Pro using python scripts, and have been working well. We recently updated the servers from Pro V1.4.1 to Pro 2.0, and are using the Runtime version 100.1. After doing so, the geodatabase files no longer render all the point features in a runtime app. The geodatabase has data in the tables, as viewed through SQLite, and features can be found using the search tool in our app (and the search zooms to the correct location), so it is not a case of the data being somehow truncated.
The geodatabase files generated are rather large (2.4 to 3.3 GB), but I have not seen anything indicating that there is a size limit on SQLite files. It does not seem to matter if I generate the mobile packages via script or directly from ArcGIS Pro. I also created a smaller Pro project with only a few layers - that one displays all features as expected. Other, smaller geodatabase files show some point features but not all.
Has anyone had a similar situation, and if so how can it be remedied?