I'm starting to think that what Des is doing in the alt-timeline is the mission that Widmore had planned for him and is the weapon to defeat Flocke- i.e. that test blast of magnetic energy was not an experiment but instead served to open a link for Des btwn the two worlds; Widmore may even have intentionally set up things because he wanted Des to get "kidnapped".
All-in-all I have the sneaky suspicion that Widmore's plan against Flocke is already in motion..
I think Flocke knows this, which is why he threw him down the well.
Of course, if Des is a threat, why didn't Flocke go all smokey on him and kill him?