diff --git a/api/src/org/labkey/api/query/AbstractQueryImportAction.java b/api/src/org/labkey/api/query/AbstractQueryImportAction.java
index e5ada4d6baa..1919ba17cac 100644
--- a/api/src/org/labkey/api/query/AbstractQueryImportAction.java
+++ b/api/src/org/labkey/api/query/AbstractQueryImportAction.java
@@ -628,7 +628,7 @@ else if (!dataFileDir.exists())
             //di = wrap(di, ve);
             //importData(di, ve);
 
-            configureLoader(loader);
+            configureLoader(loader, _target, getRenamedColumns(), allowLineageColumns(), getLineageImportAliases(), getOptionParamsMap());
 
             TransactionAuditProvider.TransactionAuditEvent auditEvent = null;
             if (behaviorType != null && behaviorType != AuditBehaviorType.NONE)
@@ -669,13 +669,12 @@ else if (!dataFileDir.exists())
 
     }
 
-    protected void configureLoader(DataLoader loader) throws IOException
+    public static void configureLoader(DataLoader loader, @Nullable TableInfo target, @Nullable Map<String, String> renamedColumns, boolean allowLineageColumns, @Nullable Set<String> lineageAliasNames, @Nullable Map<Params, Boolean> optionParamsMap) throws IOException
     {
-        configureLoader(loader, _target, getRenamedColumns(), allowLineageColumns(), null);
-    }
+        // Issue 53804: When updating or adding samples across different sample types, the strings 'Yes' and 'No' are converted to their boolean values
+        if (loader != null && optionParamsMap != null && optionParamsMap.getOrDefault(Params.crossTypeImport, false))
+            loader.setInferTypes(false);
 
-    public static void configureLoader(DataLoader loader, @Nullable TableInfo target, @Nullable Map<String, String> renamedColumns, boolean allowLineageColumns, @Nullable Set<String> lineageAliasNames) throws IOException
-    {
         //apply known columns so loader can do better type conversion
         if (loader != null && target != null)
             loader.setKnownColumns(target.getColumns());
diff --git a/api/src/org/labkey/api/query/QueryImportPipelineJob.java b/api/src/org/labkey/api/query/QueryImportPipelineJob.java
index 59e1c734440..fd51038f5c2 100644
--- a/api/src/org/labkey/api/query/QueryImportPipelineJob.java
+++ b/api/src/org/labkey/api/query/QueryImportPipelineJob.java
@@ -294,7 +294,7 @@ public void run()
 
             loader = DataLoader.get().createLoader(_importContextBuilder.getPrimaryFile(), _importContextBuilder.getFileContentType(), _importContextBuilder.isHasColumnHeaders(), null, null);
 
-            AbstractQueryImportAction.configureLoader(loader, target, _importContextBuilder.getRenamedColumns(), _importContextBuilder.allowLineageColumns(), _importContextBuilder.getLineageImportAliases());
+            AbstractQueryImportAction.configureLoader(loader, target, _importContextBuilder.getRenamedColumns(), _importContextBuilder.allowLineageColumns(), _importContextBuilder.getLineageImportAliases(), _importContextBuilder.getOptionParamsMap());
 
             TransactionAuditProvider.TransactionAuditEvent auditEvent = null;
 
diff --git a/experiment/src/org/labkey/experiment/ExpDataIterators.java b/experiment/src/org/labkey/experiment/ExpDataIterators.java
index 1bdb4385312..d2743681f91 100644
--- a/experiment/src/org/labkey/experiment/ExpDataIterators.java
+++ b/experiment/src/org/labkey/experiment/ExpDataIterators.java
@@ -2555,7 +2555,7 @@ private int _importSplitFile(TypeData typeData, File splitFile, Container dataCo
                 else
                     aliasNames = new CaseInsensitiveHashSet(((ExpDataClass) typeData.dataType).getImportAliases().keySet());
                 // We do not need to configure the loader for renamed columns as that has been taken care of when writing the file.
-                configureLoader(loader, dataTable, null, true, aliasNames);
+                configureLoader(loader, dataTable, null, true, aliasNames, null /* Not needed since partition is not a cross type import*/);
                 if (loader instanceof TabLoader tabLoader)
                     tabLoader.setIncludeComments(true); // don't skip lines that starts with "#" (if the original file is Excel)
                 return updateService.loadRows(_user, dataContainer, loader, _context, null);
diff --git a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java
index 5a9adc924b4..67c15cdc4cf 100644
--- a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java
+++ b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java
@@ -4502,13 +4502,6 @@ protected JSONObject createSuccessResponse(int rowCount)
             return json;
         }
 
-        @Override
-        protected void configureLoader(DataLoader loader) throws IOException
-        {
-            if (getOptionParamValue(Params.crossTypeImport))
-                loader.setInferTypes(false);
-            configureLoader(loader, _target, getRenamedColumns(), allowLineageColumns(), getLineageImportAliases());
-        }
     }
 
     public abstract static class AbstractExpDataImportAction extends AbstractQueryImportAction<QueryForm>
@@ -4667,12 +4660,6 @@ public void addNavTrail(NavTree root)
             root.addChild("Import Data");
         }
 
-        @Override
-        protected void configureLoader(DataLoader loader) throws IOException
-        {
-            configureLoader(loader, _target, getRenamedColumns(), allowLineageColumns(), getLineageImportAliases());
-        }
-
     }
 
     @RequiresPermission(UpdatePermission.class)