We’re working to add support for % and # characters in file and folder names in SharePoint and OneDrive for Business.
As part of this, we’re providing an early heads-up around some plans to add new file and folder APIs for this support. Please check out the blog post with details here -- in a nutshell, we're introducing a new strongly-typed object for developers to work with their file and folder URLs around (as compared to Strings). If you work with files against SharePoint/OneDrive, you'll want to analyze and inventory entry points where you work with file and folder names. Over the coming weeks, we’ll work to add more guidance and details around the APIs as they become finalized. Look forward to your feedback around these changes.
-- Mike Ammerlaan, Office Ecosystem Marketing team