It is not possible to change the passport during a SCHENGEN visa application processing.
In general visa applications for a stay for more than 90 days should be submitted with the passport you want to travel with.
If e.g. after a marriage a new passport will be applied for during the processing of a visa application, the visa application may exceptionally be submitted with the old passport, if it is still sufficiently valid for the visa processing (it must be valid for at least another 3 months on the date the visa appcliation is submitted and must contain two empty pages).
If, during the visa processing, a new passport is submitted with which you want to travel to Germany, then an additional processing time of one week after the general processing is finished has to be expected before the visa can be issued.