The schools of tropical medicine will of course be excellent sources of uptodate antimalarial advice but may well not be the best source of advice on taking antimalarials vs your professional aircrew status. I would suggest you ask an AME or go to the CAA for the "horses-mouth answer".
In the RAF our approach to mefloquine, which is probably the best A/M for where you are going, is that aircrew are not to fly for 3 months after taking it. (if they went on detatchment/holiday while on a ground tour for instance and were given it.) problem ia that Mefloquine has a very long half-life in the body (21 days springs to mind).
This is good advice, but you should confirm it is acceptable to your regulating authority first!
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