When using the geodatabase SDE reader (ESRI) or shapefile reader, the geometry of the polygon feature class does not appear correctly. Recent edits to the SDE data (v10.3.1) are not reflected
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Just wondering:
In the topic you mention two different readers, did you make sure that the shapefile was extracted from the database at the same time as you were reading it with FME?
Or have the edits taken place in a version and not been committed to the original data base?
Are you reading a older version / timestamp of the ArcSDE database?