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Turns out that this is just a by-product of paging. The missing resources are after the initial 10 so they will appear on the next page. Adding a _count parameter to make this easier.
From David Hay:
[2015-04-03, 11:04:19 PM] David Hay: http://fhirtest.uhn.ca/baseDstu2/ClinicalImpression?patient=1702
[2015-04-03, 11:04:32 PM] David Hay: returns 2 ClinicalImpressions (as it should)
[2015-04-03, 11:04:47 PM] David Hay: http://localhost:9002/getAllResources/1702
[2015-04-03, 11:04:51 PM] David Hay: only has 1...
[2015-04-04, 2:50:42 AM] David Hay: sorry - should hav ebeen
[2015-04-04, 2:50:42 AM] David Hay: http://fhirtest.uhn.ca/baseDstu2/Patient/1702/$everything
[2015-04-04, 2:51:03 AM] David Hay: (the first one was my proxy)
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