Hi Ryan,
If you want to check for unique values in all your records (i.e >1000) then try this..
Use the queryIds(query, callback?, errback?) method on the feature layer. This method has no limit to the number of records returned from the server + it will return an array of all the object_ids present in your feature class. Once you get the length of all the records present in your feature class, use this object_id array to query for distinct values and populate your final array.
For eg: I have an array length of object_ids = 2500 and at the same time, I'm also aware of the limit of records return from the ArcGIS Server (the default is 1000).
So ill query the first 1000 then the next and then the remain... and in each query ill get the distinct values and sort it in an array.
You will have to implement a logic by which this looping query is done in packets like (1-999,1000-1999,2000-2500).
Regards,
Nigel.