VFS would check paper applications to ensure they are complete before they accept them so it might be a bit confusing why your application is returned. Did they also return your passport and other documents? You said your online application shows it's still in process, what does it show on the view your submitted application option?... anyway, you will find out what exactly is going on with your application once they reply to your CSE. You could also opt to call/email the VOI have already sent an email to the embassy and also sent them an enquiry via webform.I hope they will respond.
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