I just did a small test,
1> I added an entry through the Wbl contrib reject page and issued the update command from the contrib.
2> Manually checked the /var/qmail/control/badmailfrom file with Nano (in the command line) and the entry had been added.
3> Added another entry directly in the file with Nano.
4> Check the entries in the Wbl contrib panel and of course could not see the manually added entry.
5> deleted the entry I could see that had been added in the Wbl contrib panel and issued the update command.
6> rechecked the file with Nano and found that is was empty.
Conclusion,
If there are no other template fragments that are adding entries into that file, it can be emptied by issuing the update command from the Wbl contrib, This will remove ALL the entries so if you have some you want to keep, make a list and add them in the contrib so they will be saved back to that file.
You need to find out where the entries that are there are coming from