diff --git a/cli/config.py b/cli/config.py
index 026047f5..69b9c5ea 100644
--- a/cli/config.py
+++ b/cli/config.py
@@ -263,7 +263,7 @@ def __prep_json_for_write(json_data: types.ObjectJsonRepr, export_settings: type
         json_data = utilities.remove_nones(json_data)
         if not export_settings.get(EXPORT_EMPTY, False):
             log.debug("Removing empties")
-            json_data = utilities.clean_data(json_data, remove_empty=True)
+            json_data = utilities.clean_data(json_data, remove_empty=False)
     return json_data
 
 
diff --git a/sonar/applications.py b/sonar/applications.py
index 55eb679f..326e643e 100644
--- a/sonar/applications.py
+++ b/sonar/applications.py
@@ -604,9 +604,18 @@ def search_by_name(endpoint: pf.Platform, name: str) -> dict[str, Application]:
 def convert_app_json(old_app_json: dict[str, Any]) -> dict[str, Any]:
     """Converts sonar-config old JSON report format to new format for a single application"""
     new_json = common_json_helper.convert_common_fields(old_app_json.copy())
-    if "branches" in old_app_json:
-        new_json["branches"] = util.dict_to_list(old_app_json["branches"], "name")
-    return new_json
+    if "branches" not in new_json:
+        return new_json
+    for br, data in new_json["branches"].items():
+        if "projects" not in data:
+            continue
+        new_json["branches"][br] = util.order_dict(data, ["name", "isMain", "projects"])
+        new_json["branches"][br]["projects"] = util.dict_to_list(new_json["branches"][br]["projects"], "key", "branch")
+        for proj_data in new_json["branches"][br]["projects"]:
+            if proj_data.get("branch", None) in ("__default__", c.DEFAULT_BRANCH):
+                proj_data.pop("branch")
+    new_json["branches"] = util.sort_list_by_key(util.dict_to_list(new_json["branches"], "name"), "name", "isMain")
+    return util.order_dict(new_json, ["key", "name", "visibility", "tags", "branches", "permissions"])
 
 
 def convert_apps_json(old_json: dict[str, Any]) -> dict[str, Any]:
diff --git a/sonar/util/portfolio_helper.py b/sonar/util/portfolio_helper.py
index 68397d52..41317460 100644
--- a/sonar/util/portfolio_helper.py
+++ b/sonar/util/portfolio_helper.py
@@ -21,6 +21,7 @@
 
 from typing import Any
 from sonar import utilities as util
+from sonar.util import constants as c
 from sonar.util import common_json_helper
 
 
@@ -29,11 +30,41 @@ def convert_portfolio_json(old_json: dict[str, Any]) -> dict[str, Any]:
     new_json = common_json_helper.convert_common_fields(old_json.copy())
     if "projects" in new_json:
         new_json["projects"] = common_json_helper.convert_common_fields(new_json["projects"])
+        if "manual" in new_json["projects"]:
+            projs = {}
+            for k, v in new_json["projects"]["manual"].items():
+                projs[k] = {"key": k, "branches": sorted(["" if e == c.DEFAULT_BRANCH else e for e in util.csv_to_list(v)])}
+                if projs[k]["branches"] == [""]:
+                    projs[k].pop("branches", None)
+            new_json["projectSelection"] = {"manual": new_json["projects"]}
+            new_json["projectSelection"]["manual"] = util.dict_to_list(projs, "key", "branches")
+        elif "regexp" in new_json["projects"]:
+            new_json["projectSelection"] = "regexp"
+            new_json["projectSelection"] = {"regexp": new_json["projects"]["regexp"]}
+            if new_json["projects"].get("branch", c.DEFAULT_BRANCH) != c.DEFAULT_BRANCH:
+                new_json["projectSelection"]["branch"] = new_json["projects"]["branch"]
+        elif "tags" in new_json["projects"]:
+            new_json["projectSelection"] = {"tags": new_json["projects"]["tags"]}
+            if new_json["projects"].get("branch", c.DEFAULT_BRANCH) != c.DEFAULT_BRANCH:
+                new_json["projectSelection"]["branch"] = new_json["projects"]["branch"]
+        elif "rest" in new_json["projects"]:
+            new_json["projectSelection"] = {"rest": True}
+            if new_json["projects"].get("branch", c.DEFAULT_BRANCH) != c.DEFAULT_BRANCH:
+                new_json["projectSelection"]["branch"] = new_json["projects"]["branch"]
+        new_json.pop("projects")
+    if "applications" in new_json:
+        for k, v in new_json["applications"].items():
+            new_json["applications"][k] = {"key": k, "branches": sorted(["" if e == c.DEFAULT_BRANCH else e for e in util.csv_to_list(v)])}
+            if new_json["applications"][k]["branches"] == [""]:
+                new_json["applications"][k].pop("branches", None)
+        new_json["applications"] = util.dict_to_list(new_json["applications"], "key", "branches")
+
     for key in "children", "portfolios":
         if key in new_json:
             new_json[key] = convert_portfolios_json(new_json[key])
     if "branches" in old_json:
         new_json["branches"] = util.dict_to_list(old_json["branches"], "name")
+    new_json = util.order_keys(new_json, "key", "name", "visibility", "projectSelection", "applications", "portfolios", "permissions")
     return new_json