I added them to the fpz file with a text editor and both Inkscape and Frtizing take them from there. I'm not sure exactly where Fritzing stores the numbers, I think it is in a database file somewhere. If you don't mind losing all the context you can delete the two user data files and start again which will reset all the numbers. On windows they are in
C;\Users\User_name\AppData\roaming\Fritzing and
c:\Users\user_name\My Documents\Fritizing
(where user_name is your windows user name). The AppData one is a hidden file so you need to enable show hidden files in explorer to see it. If you delete both directories Fritzing will recreate them when it starts with no memory of any part numbers. I do this fairly often (by moving both directories to a different file name usually so I don' t lose all the current parts) as it is possible to hang Fritzing if you screw up editing the files badly enough and then the only cure is to delete those two directories. Once you have the part running correctly move the saved directories back to the original file names and add your now stable part.