Answer
If re-cloning the repository into the project didn't fix it, try this: create a brand-new project with the same name in a different location, then copy that new project's nbproject/project.properties file into your existing (broken) project's same location, overwriting the old one. This has resolved exactly this kind of database-connection-won't-save issue after a Developer Studio upgrade, likely because the new project generates a clean project.properties file that the upgraded tool version can read/write correctly.