Unfortunately, it isn't possible to access/modify the pattern data (it's no longer in the same format as in the file). But it is possible to change the playback order of the patterns via the BASS_TAG_MUSIC_ORDERS "tag". That gives a pointer to the order list, which you can change. You can get the length of the list (number of orders) from BASS_ChannelGetLength.
If you want to make more elaborate changes, perhaps you could keep a copy of the file in memory for that, and pass it to BASS_MusicLoad again after changes?