I'm not really sure what's going on here - I have a web feature service in my map that I have filtered by a definition query. The filter leaves 52 records. When I R click > Data > Export Features, it informs me that there are 19,619 records to be processed, and sure enough, it exports those 19,619. 19,619 is not the full number of features, either; that's the number that results from a different query, so what gives? Clicking refresh doesn't change anything.
Seems to be related to the fact that it's also a selection layer - I cleared the selection, and it now responds to the definition query, but now I have to deal with the fact that I'm getting extra records that I had excluded by making it a selection layer.