diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
index dd71d3920cb..1ecbd6db105 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
@@ -334,6 +334,16 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 						continue;
 					}
 					nextId = nextValue.getReferenceElement();
+
+					/*
+					 * This can only really happen if the DAO is being called
+					 * programatically with a Bundle (not through the FHIR REST API)
+					 * but Smile does this 
+					 */
+					if (nextId.isEmpty() && nextValue.getResource() != null) {
+						nextId = nextValue.getResource().getIdElement();
+					}
+					
 					if (nextId.isEmpty() || nextId.getValue().startsWith("#")) {
 						// This is a blank or contained resource reference
 						continue;
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
index b4017a47416..56400d4f9e5 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
@@ -273,19 +273,24 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 			// Notify interceptors
 			IdDt idToDelete = entity.getIdDt();
-			ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, idToDelete.getResourceType(), idToDelete);
-			notifyInterceptors(RestOperationTypeEnum.DELETE, requestDetails);
-
+			if (theRequestDetails != null) {
+				ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, idToDelete.getResourceType(), idToDelete);
+				notifyInterceptors(RestOperationTypeEnum.DELETE, requestDetails);
+			}
+			
 			// Perform delete
 			Date updateTime = new Date();
 			updateEntity(null, entity, updateTime, updateTime);
 
 			// Notify JPA interceptors
 			T resourceToDelete = toResource(myResourceType, entity, false);
-			theRequestDetails.getRequestOperationCallback().resourceDeleted(resourceToDelete);
-			for (IServerInterceptor next : getConfig().getInterceptors()) {
-				if (next instanceof IJpaServerInterceptor) {
-					((IJpaServerInterceptor) next).resourceDeleted(requestDetails, entity);
+			if (theRequestDetails != null) {
+				theRequestDetails.getRequestOperationCallback().resourceDeleted(resourceToDelete);
+				ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, idToDelete.getResourceType(), idToDelete);
+				for (IServerInterceptor next : getConfig().getInterceptors()) {
+					if (next instanceof IJpaServerInterceptor) {
+						((IJpaServerInterceptor) next).resourceDeleted(requestDetails, entity);
+					}
 				}
 			}
 			for (IServerInterceptor next : getConfig().getInterceptors()) {
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3Test.java
index b6c9bf688d4..19ea6a484fb 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3Test.java
@@ -542,6 +542,60 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 		}
 	}
 
+	@Test
+	public void testTransactionWithReferenceUuid() {
+		Bundle request = new Bundle();
+
+		Patient p = new Patient();
+		p.setActive(true);
+		p.setId(IdType.newRandomUuid());
+		request.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.POST).setUrl(p.getId());
+		
+		Observation o = new Observation();
+		o.getCode().setText("Some Observation");
+		o.getSubject().setReference(p.getId());
+		request.addEntry().setResource(o).getRequest().setMethod(HTTPVerb.POST);
+
+		Bundle resp = mySystemDao.transaction(mySrd, request);
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
+		
+		String patientId = new IdType(resp.getEntry().get(0).getResponse().getLocation()).toUnqualifiedVersionless().getValue();
+		assertThat(patientId, startsWith("Patient/"));
+		
+		SearchParameterMap params = new SearchParameterMap();
+		params.setLoadSynchronous(true);
+		params.add("subject", new ReferenceParam(patientId));
+		IBundleProvider found = myObservationDao.search(params);
+		assertEquals(1, found.size().intValue());
+	}
+
+	@Test
+	public void testTransactionWithReferenceResource() {
+		Bundle request = new Bundle();
+
+		Patient p = new Patient();
+		p.setActive(true);
+		p.setId(IdType.newRandomUuid());
+		request.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.POST).setUrl(p.getId());
+		
+		Observation o = new Observation();
+		o.getCode().setText("Some Observation");
+		o.getSubject().setResource(p);
+		request.addEntry().setResource(o).getRequest().setMethod(HTTPVerb.POST);
+
+		Bundle resp = mySystemDao.transaction(mySrd, request);
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
+		
+		String patientId = new IdType(resp.getEntry().get(0).getResponse().getLocation()).toUnqualifiedVersionless().getValue();
+		assertThat(patientId, startsWith("Patient/"));
+		
+		SearchParameterMap params = new SearchParameterMap();
+		params.setLoadSynchronous(true);
+		params.add("subject", new ReferenceParam(patientId));
+		IBundleProvider found = myObservationDao.search(params);
+		assertEquals(1, found.size().intValue());
+	}
+
 	@Test
 	public void testTransactionCreateInlineMatchUrlWithOneMatch() {
 		String methodName = "testTransactionCreateInlineMatchUrlWithOneMatch";
diff --git a/src/changes/changes.xml b/src/changes/changes.xml
index 2adefcf2365..913ce9ba185 100644
--- a/src/changes/changes.xml
+++ b/src/changes/changes.xml
@@ -52,6 +52,11 @@
 				Prevent duplicates in $everything query response in JPA server. Thanks to @vlad-ignatov 
 				for reporting!
 			</action>
+			<action type="fix">
+				Fix issue in calling JPA server transactions programmatically where resources
+				are linked by object reference and not by ID where indexes were not correctly
+				generated. This should not affect most users.
+			</action>
 		</release>
 		<release version="2.5" date="2017-06-08">
 			<action type="fix">