@Raymundo.Cassani
Thank you for your quick response!
I verified the write permission for the aforementioned folders. They are all inctact.
While I am able to create a new protocol and do all the processing, I lose the access once I close the application and reopen it. Not sure why would that happen!
One of the temporary soultion I found is to export the the corrupted protocol into a zip folder (through Brainstorm), detach and delete the corrupted protocol, and import the zip folder again. This works as along as app is closed again. However, it may not be a feasible solution especilly for a large protocol with all the functional data added.