The index key order is not maintained. It seems to be in alphabetical order when ingest gets it. I suspect the agent is at fault, but more investigation is needed to confirm.

In Mongo:
db.a.ensureIndex(

{"Location" : "2d", "CreatedBy.Impersonate.CommunityType" : 1 , "CreatedTime" : 1 , "DeletedTime" : 1 , "Status" : 1 , "_t" : 1}

)

In sync metadata:
"key" :

{ "CreatedBy.Impersonate.CommunityType" : 1 , "CreatedTime" : 1 , "DeletedTime" : 1 , "Location" : "2d" , "Status" : 1 , "_t" : 1}