Taiwan -> Pudong Shanghai -> Sydney

I am an India passport holder, living in Taiwan.I am travelling to sydney via Shanghai. For going there is 3 hours layover and coming back flight has 16 hours layover.
Am I eligible to do transfer with china entry permit.
FYI 2 months back, airline didn't let me board flight from Taiwan to Sydney via Shenzhen, China. They said at Shenzhen, international transfer is not allowed without china entry permit.
Correction. "without* china visa"