Arrival in Hongkong, 5 days in Shenzen, return via Hongkong from Shanghai - possible?

I am confused about the 24h rule. I arrived in Hongkong, and entered mainland China in Shenzen with a single entry visa. My return trip home to Germany is via Shanghai, where I will spend one night (less than 24h altogether). However, I have a flight from Hongkong to Shanghai, and not Shenzen, meaning I will leave China and re-enter. Is this possible?