Yes, you should better calculate the PENRM and PERM values manually from the lower heating values of the corresponding product inputs. You can manually insert the elementary flows for PENRM and PERM into you EPD modules, so that they appear in the PENRM and PERM results, and so that PENRE and PERE is automatically calculated as the difference between PENRE = PENRT - PENRM and PERE = PERT - PERM.
For further guidance, you should check the rules from the program operator where you will publish the EPD. Sometimes they have on their website, or in the PCRs examples and rules on how to evaluate the PENRM and PERM indicators manually for each EPD module. We cannot automate this anymore, since most program operators and therefore most reviewers will ask to have this approximation only in the foreground (manually calculated in the foreground) and not over the background database like ecoinvent.