diff --git a/input/fsh/examples/0001-add-condition-transaction-example.1.fsh b/input/fsh/examples/0001-add-condition-transaction-example.fsh
similarity index 98%
rename from input/fsh/examples/0001-add-condition-transaction-example.1.fsh
rename to input/fsh/examples/0001-add-condition-transaction-example.fsh
index a210650..f00cfc8 100644
--- a/input/fsh/examples/0001-add-condition-transaction-example.1.fsh
+++ b/input/fsh/examples/0001-add-condition-transaction-example.fsh
@@ -8,7 +8,7 @@ Alias: $DataOperation = http://terminology.hl7.org/CodeSystem/v3-DataOperation
 Alias: $CareConnect-SDSJobRoleName-1 = https://fhir.hl7.org.uk/STU3/CodeSystem/CareConnect-SDSJobRoleName-1
 Alias: $RARecord-AdjustmentCategory-1 = https://fhir.nhs.uk/STU3/CodeSystem/RARecord-AdjustmentCategory-1
 
-Instance: 0001-add-condition-transaction-example.1
+Instance: 0001-add-condition-transaction-example
 InstanceOf: Bundle
 Usage: #example
 * type = #transaction
diff --git a/input/fsh/examples/0002-add-condition-transaction-example.2.fsh b/input/fsh/examples/0002-add-condition-transaction-example.fsh
similarity index 98%
rename from input/fsh/examples/0002-add-condition-transaction-example.2.fsh
rename to input/fsh/examples/0002-add-condition-transaction-example.fsh
index f96190a..96e0ba6 100644
--- a/input/fsh/examples/0002-add-condition-transaction-example.2.fsh
+++ b/input/fsh/examples/0002-add-condition-transaction-example.fsh
@@ -8,7 +8,7 @@ Alias: $DataOperation = http://terminology.hl7.org/CodeSystem/v3-DataOperation
 Alias: $CareConnect-SDSJobRoleName-1 = https://fhir.hl7.org.uk/STU3/CodeSystem/CareConnect-SDSJobRoleName-1
 Alias: $RARecord-AdjustmentCategory-1 = https://fhir.nhs.uk/STU3/CodeSystem/RARecord-AdjustmentCategory-1
 
-Instance: 0002-add-condition-transaction-example.2
+Instance: 0002-add-condition-transaction-example
 InstanceOf: Bundle
 Usage: #example
 * type = #transaction
diff --git a/input/queries/0002-add-condition-transaction-example.1.md b/input/queries/0002-add-condition-transaction-example.1.md
new file mode 100644
index 0000000..0108957
--- /dev/null
+++ b/input/queries/0002-add-condition-transaction-example.1.md
@@ -0,0 +1 @@
+Patient?identifier=9912003888&_revinclude=Consent:patient&_revinclude=Flag:patient&_revinclude=Condition:patient
diff --git a/input/queries/0002-add-condition-transaction-example.2.md b/input/queries/0002-add-condition-transaction-example.2.md
index 0108957..b294a31 100644
--- a/input/queries/0002-add-condition-transaction-example.2.md
+++ b/input/queries/0002-add-condition-transaction-example.2.md
@@ -1 +1 @@
-Patient?identifier=9912003888&_revinclude=Consent:patient&_revinclude=Flag:patient&_revinclude=Condition:patient
+Patient?identifier=9912003888&_revinclude=Consent:patient
diff --git a/scripts/run-examples.sh b/scripts/run-examples.sh
index 1769513..b68bc46 100755
--- a/scripts/run-examples.sh
+++ b/scripts/run-examples.sh
@@ -1,7 +1,6 @@
 #!/bin/bash
 
-# TODO The order of the examples may be important depending on the queries.  Would there be a tidy way of chaining them and makes the depedancies
-# clear, explicit and useful in the guidance?
+# TODO Document how to organise the examples and queries in the IG
 # Probably makes more sense just to describe the queries and add output in statically, rather trying to combine integrations testing
 # into the build of the IG.  See if it serves as a useful example... 
 
@@ -17,7 +16,7 @@ for EXAMPLE in ./input/fsh/examples/*; do
   EXAMPLE=$(echo $EXAMPLE | awk -F '/' '{print $5}' | awk -F '.' '{print $1}');
 
   # This relies on SUSHI having been ran to generate JSON representations of the resources.
-  GENERATED=$(echo ./fsh-generated/resources/*${EXAMPLE%.*}*);
+  GENERATED=$(echo ./fsh-generated/resources/*$EXAMPLE*);
 
   # Sushi will prepend the name of the Resource, which will be used in the server calls.
   RESOURCE_NAME=$(echo $GENERATED | awk -F '/' '{print $4}' | awk -F '-' '{print $1}');
@@ -31,10 +30,15 @@ for EXAMPLE in ./input/fsh/examples/*; do
   # Post the resource
   curl -X POST -H $HEADERS -d @${GENERATED} $SERVER_BASE$RESOURCE_NAME;
 
-  # Filename of query (minus extension) must match the filename of the example posted.
-  QUERY=$(cat ./input/queries/${EXAMPLE%.*}*);
+  for QUERY_FILE in ./input/queries/$EXAMPLE*; do
+    # Filename of query (minus extension) must match the filename of the example posted.
+    QUERY=$(cat ${QUERY_FILE%.*}*);
 
-  # Run corresponding query, change the ID of the bundle to something readable and output to resources in input to be included in IG build
-  curl $SERVER_BASE$QUERY | jq '.id = "QUERY-OUTPUT--'${EXAMPLE%.*}'"' > ./input/resources/QUERY-OUTPUT--${EXAMPLE%.*}.json
+    # Strip the path
+    QUERY_FILE=$(echo $QUERY_FILE | awk -F '/' '{print $4}');
+
+    # Run corresponding query, change the ID of the bundle to something readable and output to resources in input to be included in IG build
+    curl $SERVER_BASE$QUERY | jq '.id = "QUERY-OUTPUT--'${QUERY_FILE%.*}'"' > ./input/resources/QUERY-OUTPUT--${QUERY_FILE%.*}.json
+  done;
 
 done;
\ No newline at end of file