With Panvalet, there is no chance to export a member with expanded ++INCLUDEs with renumbering the sequence numbers of the complete exported COBOL source.
Also, there is no way to prevent the ISPF editor from automatically changing the profile settings from NUMBER ON COB to NUMBER OFF.
Currently, the edited COBOL member on PDS(E) doesn't have ascending sequence numbers in these case. So you have to go to the ISPF edit command line the first time, issue NUM ON COB and save the member. The member will automatically be renumbered. Next time the member is edited, ISPF will PICK up the COBOL settings from the profile.
Alternatively, it may be checked whether this can be done by a (site written) ISPF EDIT macro.