I just thought to share this in case someone else is having the same problem.
What happened was that I wanted to switch Blackberry phones so I backed up my previous phone using Blackberry Protect. On logging in to Blackberry Protect (on the new phone) and restoring, my BBM contacts were empty. I suspected it was because my previous phone was using BBM 7 while the new one was using BBM 8.
What I did was to downgrade the BBM 8 on the new phone to BBM 7 using the tutorial at https://www.hovatek.com/forum/thread-78.html . On restoring the Blackberry protect backup again, all my contacts appeared.