diff --git a/.github/workflows/mad_modelDiff.yml b/.github/workflows/mad_modelDiff.yml
index 17640da9f2e1..62cb57fd9353 100644
--- a/.github/workflows/mad_modelDiff.yml
+++ b/.github/workflows/mad_modelDiff.yml
@@ -12,6 +12,7 @@ on:
       - main
     paths:
       - "java/ql/src/utils/modelgenerator/**/*.*"
+      - "misc/scripts/models-as-data/*.*"
       - ".github/workflows/mad_modelDiff.yml"
 
 permissions:
@@ -61,8 +62,9 @@ jobs:
             DATABASE=$2
             cd codeql-$QL_VARIANT
             SHORTNAME=`basename $DATABASE`
-            python java/ql/src/utils/modelgenerator/GenerateFlowModel.py --with-summaries --with-sinks $DATABASE ${SHORTNAME}.temp.model.yml
-            mv java/ql/lib/ext/generated/${SHORTNAME}.temp.model.yml $MODELS/${SHORTNAME}Generated_${QL_VARIANT}.model.yml
+            python java/ql/src/utils/modelgenerator/GenerateFlowModel.py --with-summaries --with-sinks $DATABASE $SHORTNAME/$QL_VARIANT
+            mkdir -p $MODELS/$SHORTNAME
+            mv java/ql/lib/ext/generated/$SHORTNAME/$QL_VARIANT $MODELS/$SHORTNAME
             cd ..
           }
 
@@ -85,16 +87,16 @@ jobs:
           set -x
           MODELS=`pwd`/tmp-models
           ls -1 tmp-models/
-          for m in $MODELS/*_main.model.yml ; do
+          for m in $MODELS/*/main/*.model.yml ; do
             t="${m/main/"pr"}"
             basename=`basename $m`
-            name="diff_${basename/_main.model.yml/""}"
+            name="diff_${basename/.model.yml/""}"
             (diff -w -u $m $t | diff2html -i stdin -F $MODELS/$name.html) || true
           done
       - uses: actions/upload-artifact@v3
         with:
           name: models
-          path: tmp-models/*.model.yml
+          path: tmp-models/**/**/*.model.yml
           retention-days: 20
       - uses: actions/upload-artifact@v3
         with: