diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java b/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java
index 756567ed7d4..5179a03afbc 100644
--- a/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java
+++ b/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java
@@ -28,9 +28,6 @@ import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.hl7.fhir.dstu3.model.Parameters;
-import org.hl7.fhir.dstu3.model.StringType;
-import org.hl7.fhir.dstu3.model.UriType;
 import org.hl7.fhir.instance.model.api.IBaseParameters;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
@@ -82,10 +79,17 @@ public class UploadTerminologyCommand extends BaseCommand {
 		IGenericClient client = super.newClient(theCommandLine);
 		IBaseParameters inputParameters;
 		if (ctx.getVersion().getVersion() == FhirVersionEnum.DSTU3) {
-			Parameters p = new Parameters();
-			p.addParameter().setName("url").setValue(new UriType(termUrl));
+			org.hl7.fhir.dstu3.model.Parameters p = new org.hl7.fhir.dstu3.model.Parameters();
+			p.addParameter().setName("url").setValue(new org.hl7.fhir.dstu3.model.UriType(termUrl));
 			for (String next : datafile) {
-				p.addParameter().setName("localfile").setValue(new StringType(next));
+				p.addParameter().setName("localfile").setValue(new org.hl7.fhir.dstu3.model.StringType(next));
+			}
+			inputParameters = p;
+		} else if (ctx.getVersion().getVersion() == FhirVersionEnum.R4) {
+			org.hl7.fhir.r4.model.Parameters p = new org.hl7.fhir.r4.model.Parameters();
+			p.addParameter().setName("url").setValue(new org.hl7.fhir.r4.model.UriType(termUrl));
+			for (String next : datafile) {
+				p.addParameter().setName("localfile").setValue(new org.hl7.fhir.r4.model.StringType(next));
 			}
 			inputParameters = p;
 		} else {
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
index 77e07267064..92a9cf8808c 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
@@ -837,15 +837,16 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
 			return;
 		} else if (myDeferredConcepts.isEmpty() && myConceptLinksToSaveLater.isEmpty()) {
 			processReindexing();
-			return;
 		}
 
 		TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
 		tt.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
-		tt.execute(t -> {
-			processDeferredConcepts();
-			return null;
-		});
+		if(!myDeferredConcepts.isEmpty() || !myConceptLinksToSaveLater.isEmpty()) {
+			tt.execute(t -> {
+				processDeferredConcepts();
+				return null;
+			});
+		}
 
 		if (myDeferredValueSets.size() > 0) {
 			tt.execute(t -> {
diff --git a/src/changes/changes.xml b/src/changes/changes.xml
index 3812fc56b6a..5bbc4f7c607 100644
--- a/src/changes/changes.xml
+++ b/src/changes/changes.xml
@@ -108,6 +108,17 @@
 				unexpectedly resources could be left in a weird state. This has been
 				corrected.
 			</action>
+			<action type="fix" issue="1015">
+				A bug was fixed in the JPA terminology uploader, where it was possible
+				in some cases for some ValueSets and ConceptMaps to not be saved because
+				of a premature short circuit during deferred uploading. Thanks to 
+				Joel Schneider for the pull request!
+			</action>
+			<action type="fix" issue="969">
+				A bug in the HAPI FHIR CLI was fixed, where uploading terminology for R4
+				could cause an error about the incorrect FHIR version. Thanks to 
+				Rob Hausam for the pull request!
+			</action>
 		</release>
 		<release version="3.4.0" date="2018-05-28">
 			<action type="add">