A116: Master of Fire And Darkness simply turns those two powers into independent encounter powers. Their use is no longer granted by your Llothtouched racial ability, but rather by Master of Fire And Darkness.
This makes Lolth Blessed useless. RAI I'd permit it to either recharge both, or at the very least one.Your Lolthtouched racial trait normally lets you use either cloud of darkness or darkfire as an encounter power. Now cloud of darkness and darkfire are two separate encounter powers. You can use each power once per encounter.
Alternatively, maybe Llothtouched and MoFAD let you use them 3 times total per encounter, if we read the "Now" clause as not removing/changing the Llothtouched-can-let-you-use-these-encounter-powers text.
A117 You no longer have a Llothtouched Racial Power. You have two independent encounter powers granted by Master of Fire and Darkness. It is unclear to me if by RAW you'd expend the (now otherwise useless) Llothtouched Racial Power encounter use to trigger this (!), or you have nothing to expend.