Welcome back to the Wefugees Community and thank you for reaching out to us again.
Even if your partner does not hold the original passport, he can still get accepted as refugee in Germany. Instead, he needs to present his story, his identity and his reasons to apply for asylum credibly and plausibly to the authorities (BAMF). Depending on the type of recognition he may receive, he could be asked to apply for a new passport at the embassy of his country of origin at a later stage and AFTER the asylum process. As long as the decision is pending, he puts his application at risk when seeking services from authorities of his country of origin.
Regarding your second question: No, in general it is not possible to apply for asylum in another EU country after a negative outcome in the first. Even though Switzerland is not an EU member, the EU and Switzerland (as also Norway, for instance) share a common asylum system which includes i.e. the Dublin regulation.
I hope this helps and please don't hesitate to get back to us with any further questions.
All the best,