If I understand the question, you want to get stories that are currently accepted, but you want that the returned results include snapshots from the time when they were not accepted. Before you write code, you may test an equivalent query in the browser and see if the results look as expected.
Here is an example - you will have to change OIDs.
https://rally1.rallydev.com/analytics/v2.0/service/rally/workspace/12352608129/artifact/snapshot/query.js?find={"_ProjectHierarchy":12352608219,"_TypeHierarchy":"HierarchicalRequirement","ScheduleState":"Accepted",_ValidFrom:{$gte: "2013-11-01",$lt: "2014-01-01"}}},sort:[{"ObjectID": 1},{_ValidFrom: 1}]&fields=["Name","ScheduleState","PlanEstimate"]&hydrate=["ScheduleState"]
You are correct that a query like this: find={"AcceptedDate":{$gt:"2014-01-01T00:00:00.000Z"}}
will return one snapshot per story that satisfies it.
https://rally1.rallydev.com/analytics/v2.0/service/rally/workspace/12352608129/artifact/snapshot/query.js?find={"AcceptedDate":{$gt:"2014-01-01T00:00:00.000Z"}}&fields=true&start=0&pagesize=1000
but a query like this: find={"ObjectID":{$in:[16483705391,16437964257,14943067452]}}
will return the whole history of the 3 artifacts:
https://rally1.rallydev.com/analytics/v2.0/service/rally/workspace/12352608129/artifact/snapshot/query.js?find={"ObjectID":{$in:[16483705391,16437964257,14943067452]}}&fields=true&start=0&pagesize=1000
To illustrate, here are some numbers: the last query returns 17 results for me. I check each story's revision history, and the number of revisions per story are 5, 5, 7 respectively, sum of which is equal to the total result count returned by the query.
On the other hand the number of stories that meet find={"AcceptedDate":{$gt:"2014-01-01T00:00:00.000Z"}}
is 13. And the query based on the accepted date returns 13 results, one snapshot per story.