Solution
This behavior was introduced when the version control feature was added, the default save version if not going to be override or set automatically when updating to new version.
To edit, set or override the projects created in older versions the project should be saved in current LabVIEW IDE version. To achieve this, in the Project Explorer go to Project tab and then Properties. In the Save Version option select the LabVIEW version currently being used:

After doing this, the changes made in setting are going to be save.