Turns out it was the quotes in the selection syntax. This change occurred sometime between 10.1 and 10.3.1, though Esri says I was writing bad queries all along as double-quotes are a
no-no … though it looks like double-quotes are only problematic when used on joined fields in various selection queries (including definition queries—this was also causing problems in some 10.1 .mxds once we upgraded 10.3.1). I’ve removed them from my arcpy habits altogether.
This worked at 10.1 but doesn't work at 10.3.1:
arcpy.SelectLayerByAttribute_management("wellboretable_layer", "NEW_SELECTION", "\"tbl_wellbores.OBJECTID\" = 1")
This does:
arcpy.SelectLayerByAttribute_management("wellboretable_layer", "NEW_SELECTION", "tbl_wellbores.OBJECTID = 1")