I was facing same problem as I was not able to book appointment for my wife.. On scheduled date and time (yesterday), we both reached VFS Chandigarh but at the gate my wife was not allowed to go inside.. However, when I told the authorities in the Office that file no. is same and we have received BIL for both, they agreed to take biometric finger print for my wife also.. They generated appointment letter for wife on the spot and completed biometric..I was facing the same issue. I booked my Dad's Biometric appointment but was not able to book my Mom's.. emailed VFS but did on hear back for almost 10 days. Both my parents went together on Dec 7 (Dad's Bio Appointment) and showed them email sent to VFS regarding my Mom's appointment.. VFS -Jalandhar scheduled my mom's appointment on spot ..my parent's biometric was completed on same day dec 7th.. I hope this helps... every VFS branch is different..
A point worth to mention that they were more cooperative with me when I opted their Premium services for passport pick up and delivery..