There is a small open-source program that I wrote for fixing the new ONS maps so clients can download them on the fly. It is simple and straightforward. It verifies the 4 signature bytes that signify a UT package file, then it changes the appropriate flag. The flag is a 32-bit integer at offset 8. Take a look at the source if you are interested, else just run either the linux or win32 binaries.
./tagger map1.ut2 map2.ut2 ...
tagger.exe map1.ut2 map2.ut2 ...
This will tag the maps you specify.