Dear Gentle james,
Welcome back to the Wefugees Community and thank you for reaching out to us.
I assume that you applied for a residence permit according to §28 of the German Residence Act as father of a German child for the purpose of care and custody? It is a bit difficult to give an answer without knowing the whole situation, but submitting the passport will be a normal requirement for the issuing of the residence permit. From my perspective, you shouldn't worry too much and I think that the lawyer would have also explained you otherwise if he/she sees any potential issues. Would you agree dear @alla_fka?
About the length of the procedure: This varies significantly from immigration office to immigration office and I am afraid it will be not possible to give any precise answer on this.
All the best,
P.S.: I saw that you opened a second thread with similar content. In order to keep information in one place and a better overview, I closed that one. I hope this is okay for you.