diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/2843-revert-treat-canonicals-as-local.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/2843-revert-treat-canonicals-as-local.yaml
new file mode 100644
index 00000000000..47e9bb8b859
--- /dev/null
+++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/2843-revert-treat-canonicals-as-local.yaml
@@ -0,0 +1,6 @@
+---
+type: change
+issue: 2843
+title: "Reverting the change to treat canonical references as local when setting the flag `getTreatBaseUrlsAsLocal()`. This
+was added to address a limitation in `_include` that did not process references by canonical URLs. 
+The `_include` search operation now includes canonical references without special configuration."
diff --git a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
index e55f240382a..1bfa13d10d0 100644
--- a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
+++ b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
@@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.searchparam.extractor;
  * #L%
  */
 
-import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
 import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
 import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
@@ -28,6 +27,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
+import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
@@ -1415,11 +1415,6 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 			}
 		}
 
-		private boolean isOrCanBeTreatedAsLocal(IIdType theId) {
-			boolean acceptableAsLocalReference = !theId.isAbsolute() || myModelConfig.getTreatBaseUrlsAsLocal().contains(theId.getBaseUrl());
-			return acceptableAsLocalReference;
-		}
-
 		public PathAndRef get(IBase theValue, String thePath) {
 			extract(new SearchParamSet<>(),
 				new RuntimeSearchParam(null, null, "Reference", null, null, null, null, null, null, null),
diff --git a/hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/BaseStorageDao.java b/hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/BaseStorageDao.java
index 1292eb11d47..6d3b7c58010 100644
--- a/hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/BaseStorageDao.java
+++ b/hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/BaseStorageDao.java
@@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.dao;
  * #L%
  */
 
-import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.i18n.Msg;
@@ -70,7 +69,6 @@ import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
 import org.hl7.fhir.instance.model.api.IBaseReference;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.hl7.fhir.r4.model.InstantType;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.annotation.Propagation;
@@ -174,9 +172,7 @@ public abstract class BaseStorageDao {
 		verifyBundleTypeIsAppropriateForStorage(theResource);
 
 		if(!getConfig().getTreatBaseUrlsAsLocal().isEmpty()) {
-			FhirTerser terser = myFhirContext.newTerser();
-			replaceAbsoluteReferencesWithRelative(theResource, terser);
-			replaceAbsoluteUrisWithRelative(theResource, terser);
+			replaceAbsoluteReferencesWithRelative(theResource, myFhirContext.newTerser());
 		}
 
 		performAutoVersioning(theResource, thePerformIndexing);
@@ -235,27 +231,6 @@ public abstract class BaseStorageDao {
 			}
 	}
 
-	/**
-	 * Replace Canonical URI's with local references, if we find that the canonical should be treated as local.
-	 */
-	private void replaceAbsoluteUrisWithRelative(IBaseResource theResource, FhirTerser theTerser) {
-
-		BaseRuntimeElementDefinition<?> canonicalElementDefinition = myFhirContext.getElementDefinition("canonical");
-		if (canonicalElementDefinition != null) {
-			Class<? extends IPrimitiveType<String>> canonicalType = (Class<? extends IPrimitiveType<String>>) canonicalElementDefinition.getImplementingClass();
-			List<? extends IPrimitiveType<String>> canonicals = theTerser.getAllPopulatedChildElementsOfType(theResource, canonicalType);
-
-			//TODO GGG this is pretty inefficient if there are many baseUrls, and many canonicals. Consider improving.
-			for (String baseUrl : myModelConfig.getTreatBaseUrlsAsLocal()) {
-				for (IPrimitiveType<String> canonical : canonicals) {
-					if (canonical.getValue().startsWith(baseUrl)) {
-						canonical.setValue(canonical.getValue().substring(baseUrl.length() + 1));
-					}
-				}
-			}
-		}
-	}
-
 	/**
 	 * Handle {@link ModelConfig#getAutoVersionReferenceAtPaths() auto-populate-versions}
 	 * <p>