Hi @tcrossman​, it would be helpful to know the version of FME you are on as well as the version of ESRI software you are using. If this continues to be an issue a possible workaround would be to read the features using the File Geodb Open API format. This will read the features in differently than the Esri Geodatabase(File Geodb) format, but it should read them in. 

Thanks for the reply, @jennaatsafe​ . I am using FME 2022.2.0.0 Build 22743, ArcGIS Pro 2.9.6. Good point about the Open API; I will see what schema attributes and features that one produces. So far, I have not seen, nor seen documented, any FME geodatabase format atttribute for the "Annotation created with new features" annotation feature class switch. (I am, of course, also assuming here that, if there is such a format attribute, then I can set its value and include it on schema features when building a new GDB from schema features. My questions is moot, if not.)