diff --git a/examples/json_map/merge_copied.mapping.json b/examples/json_map/merge_copied.mapping.json
new file mode 100644
index 000000000..b1b30c660
--- /dev/null
+++ b/examples/json_map/merge_copied.mapping.json
@@ -0,0 +1,31 @@
+{
+    "/@default": "entry",
+    "/ENTRY[entry]/DATA[data]/current": 0,
+    "/ENTRY[entry]/DATA[data]/temperature": 0,
+    "/ENTRY[entry]/DATA[data]/voltage": 0,
+    "/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/voltage_controller/calibration_time": "/entry/instrument/environment/voltage_controller/calibration_time",
+    "/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/voltage_controller/run_control": "/entry/instrument/environment/voltage_controller/run_control",
+    "/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/voltage_controller/value": "/entry/instrument/environment/voltage_controller/value",
+    "/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/temperature_controller/calibration_time": "/entry/instrument/environment/temperature_controller/calibration_time",
+    "/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/temperature_controller/run_control": "/entry/instrument/environment/temperature_controller/run_control",
+    "/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/temperature_controller/value": "/entry/instrument/environment/temperature_controller/value",
+    "/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/current_sensor/calibration_time": "/entry/instrument/environment/current_sensor/calibration_time",
+    "/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/current_sensor/run_control": "/entry/instrument/environment/current_sensor/run_control",
+    "/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/current_sensor/value": "/entry/instrument/environment/current_sensor/value",
+    "/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/independent_controllers": ["voltage_controller", "temperature_control"],
+    "/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/measurement_sensors": ["current_sensor"],
+    "/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/NXpid[heating_pid]/description": "/entry/instrument/environment/heating_pid/description",
+    "/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/NXpid[heating_pid]/setpoint": "/entry/instrument/environment/heating_pid/setpoint",
+    "/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/NXpid[heating_pid]/K_p_value": "/entry/instrument/environment/heating_pid/K_p_value",
+    "/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/NXpid[heating_pid]/K_i_value": "/entry/instrument/environment/heating_pid/K_i_value",
+    "/ENTRY[entry]/INSTRUMENT[instrument]/ENVIRONMENT[environment]/NXpid[heating_pid]/K_d_value": "/entry/instrument/environment/heating_pid/K_d_value",
+    "/ENTRY[entry]/PROCESS[process]/program": "Bluesky",
+    "/ENTRY[entry]/PROCESS[process]/program/@version": "1.6.7",
+    "/ENTRY[entry]/SAMPLE[sample]/name": "super",
+    "/ENTRY[entry]/SAMPLE[sample]/atom_types": "Si, C",
+    "/ENTRY[entry]/definition": "NXiv_temp",
+    "/ENTRY[entry]/definition/@version": "1",
+    "/ENTRY[entry]/experiment_identifier": "dbdfed37-35ed-4aee-a465-aaa0577205b1",
+    "/ENTRY[entry]/experiment_description": "A simple IV temperature experiment.",
+    "/ENTRY[entry]/start_time": "2022-05-30T16:37:03.909201+02:00"
+}
\ No newline at end of file
diff --git a/examples/json_map/merge_partial_appdefs.mapping.json b/examples/json_map/merge_linked.mapping.json
similarity index 99%
rename from examples/json_map/merge_partial_appdefs.mapping.json
rename to examples/json_map/merge_linked.mapping.json
index f64b3d544..386779d8b 100644
--- a/examples/json_map/merge_partial_appdefs.mapping.json
+++ b/examples/json_map/merge_linked.mapping.json
@@ -18,5 +18,4 @@
     "/ENTRY[entry]/experiment_identifier": "dbdfed37-35ed-4aee-a465-aaa0577205b1",
     "/ENTRY[entry]/experiment_description": "A simple IV temperature experiment.",
     "/ENTRY[entry]/start_time": "2022-05-30T16:37:03.909201+02:00"
-
 }
\ No newline at end of file
diff --git a/examples/json_map/merged_copied.nxs b/examples/json_map/merged_copied.nxs
new file mode 100644
index 000000000..3a96de656
Binary files /dev/null and b/examples/json_map/merged_copied.nxs differ
diff --git a/examples/json_map/merged.nxs b/examples/json_map/merged_linked.nxs
similarity index 100%
rename from examples/json_map/merged.nxs
rename to examples/json_map/merged_linked.nxs
diff --git a/pynxtools/dataconverter/readers/json_map/reader.py b/pynxtools/dataconverter/readers/json_map/reader.py
index c2fc6565a..6ca463dd0 100644
--- a/pynxtools/dataconverter/readers/json_map/reader.py
+++ b/pynxtools/dataconverter/readers/json_map/reader.py
@@ -21,6 +21,7 @@
 import pickle
 import numpy as np
 import xarray
+from mergedeep import merge
 
 from pynxtools.dataconverter.readers.base.reader import BaseReader
 from pynxtools.dataconverter.template import Template
@@ -142,7 +143,7 @@ def read(self,
                 if is_hdf5:
                     hdf = hdfdict.load(file_path)
                     hdf.unlazy()
-                    data = dict(hdf)
+                    merge(data, dict(hdf))
 
         if mapping is None:
             template = Template({x: "/hierarchical/path/in/your/datafile" for x in template})