Help, can my friend use the 72 hour free transit??

I have a very important question and I'm absolutely confused right now.

My friend is visiting me in Shanghai right now and we wanna go to Hong Kong in two days will tuesday. So he still used his one time entry permit and he will be in PRC next weeks for two other day (till thursday), so we are planning to use the 72h Visa for him. But now I'm not really sure if it work out, because we booked the flight to and from Hong Kong a few days ago.

The travel plan was:
Germany - Shanghai - Hongkong - Shanghai - Germany

Is his second stay in Shanghai a transit stay?
Thanks for reply and best,
Jasmin