Problem: A GET_FEATURES query from an ArcMap Service returns only 2000 features
You can initiate a GET_FEATURES request by querying or selecting features of a map service. It is possible that the number of features returned is less than what you expected.
There is a limit to the number of features returned from a GET_FEATURES request for ArcMap Services. The default limit is 2000 features.
Solution or Workaround
If you are the administrator of an ArcMap Service you can set a new limit in the aimsamsrv.cfg configuration file found under <ArcIMS Installation>/Server/etc on Windows or <ArcIMS Installation>\etc on Unix. Change the value "2000" for <PARAMETER name="featurelimit" value="2000" /> to the new number.
Unlike ArcIMS Image Services, the featurelimit setting affects all layers of all ArcMap Services. You cannot specify different limits for different layers within an ArcMap Service of different limits for different ArcMap Services.