Hi Jonas,
no problem with generation of a JAM file from POF file at all. No magic nor a trick are necessary. Just try the following:
Open the Programmer tool in Quartus design system, load a POF file via Add file option. Then select "Create JAM, JBC, SVF or ISC File..." in File menu. In the "Create ..." dialog just select the desired file format, file name and OK. There are not any further options for JAM file format because of a JAM file with encapsulated actions. This JAM file generation can be done also without a connection to a programmer hardware.
Best regards,
Martin