Long term Malarone usage
I am a medic on a seismic crew in Sudan, have been using Malarone for the last 3 months and have not suffered any side effects. Prior to this I used mefloquine, also without side effects, but now that I am flying I prohibited from using it.
All expats on this crew are on Malorone for malaria prophylaxis and I have yet to see any side effects. Some of them have been on Malarone for over a year. Regulations about how long you may take Malarone differ from country to country, but IIRC the UK now allows the use of Malarone for up to a year.
As far as I can see from personal obsevation and the limited information available, Malarone seems to be safe for prolonged usage.
If you are worried about using Malarone for long term prophylaxis, then you can look at an alternative which is to take 100mg doxycycline daily. Be sure though to consult a health care practitioner that is familiar with tropical medicine - your own doctor may not be.
Regards and fly safely.