@Lindon I haven't had any issues using the AppData folder both for development in HISE and in the compiled plugin. It's actually nice because you don't have two sets of the same files. For example, in my code I create and store a custom settings file in the AppData folder, so when I'm developing in HISE it just writes to the same file as the compiled plugin, which is totally fine.
Is there a specific use-case you want for saving things to the Project Folder instead of the AppData folder?