first of all, you can find contact information of migration/refugee counselling offices or in Stuttgart as well as of lawyers working in this area on the Web page of Flüchtlingsrat (Refugee Councel) Baden-Württemberg: https://fluechtlingsrat-bw.de/adressen/
You can also contact Flüchtlingsrat on phone Monday, Thursday, Friday 14:00 – 16:00, Wednesday 14:00 – 17:00 (0711 / 55 32 83-4) or ask them in mail, if they can make exacter recomendation (firstname.lastname@example.org).
It is difficult to assess your situation without knowing details. The important thing is how much risk you have to be deported if you bring your passport. It depends naturally on your country of origin and on your personal situation. Naturally you can ask for prolonging your Duldung until you finish your studies. But, unlike Ausbildung, studing in the university doesn't give you a legal right for a safe Duldung. It is therefore very important to get good councelling and support.
On the other side, from the legal point of view the Ausländerbehörde has right to give you a job ban, if you don't cooperate in clearing your identity (bring no identity documents and make no visible steps to reach them). And in my experience in Baden-Württemberg they normally use this right. So if you want to have your work permission back, it is better to make at least some steps and to give proof to Ausländerbehörde. Which steps, it depends on your up-to-date situation with the documents.
Meike is not mistaken about the plans of the governing coalition to abolish the concept of "ban/prohibition to work" in Germany. It has been a part of coalition contract. But nobody knows in the moment how quickly this change can come and in what form. Perhaps they will leave some exclusions. And anywas, passing of a new bill takes time. I wouldn't perhaps wait so long, I would look if it is possible to do something to get your work permission back now. Because if you finish your studies successfully, find work in the area of your studies and wish to get a residence permit for this purpose, you definitely need a valid passport. It would be then an absolutely necessary condition.