If I fire a torpedo with Thane,

Can I use his Ability to flip a card and then use Munitions Failsafe to recover a charge?

They seem to share the same activation window.

No. Failsafe is triggered after rolling dice and is a cancellation not a modification so it happens immediately, several steps before Thane's spend could occur.

@thespaceinvader is correct. Here's the cards for text reference:

On page 9 of the Rules Reference under Dice Modification you will find Spend . The dice modification step is separate from rolling dice which means everything to do with rolling dice, including "after rolling dice" triggers, has to be completed prior to anything to do with modifying.

New RR just dropped, but dice mods are still on p9

2 hours ago, gjnido said:

They  seem  to share the same activation window. 

For further clarification on why dice mods are not in the same timing as "after rolling dice" you can turn to Timing on page 18-19 of the Rules Reference (1.0.3) where After is specified as:

"• After : The effect resolves immediately following the timing specified. "

In other words it is not simultaneous with the next step, in this case dice modification.