The flux emitter was a device that emitted flux energy, and was built by Citizen Brown, Emmett Brown's counterpart in 1931 in an alternate timeline. It was part of the chronometric analyser, which was a diagnostic device meant to help calibrate the time circuits.
Edna Strickland stole the DeLorean time machine with the flux emitters attached. When Citizen Brown faded out of existence and was replaced by Doc Brown, Doc and Marty traveled in Doc's DeLorean to 1876 to stop her. Marty attached flux overrides on the flux emitters on the DeLorean Edna was driving. This allowed Doc to control her DeLorean with his, so he accelerated to 88 m.p.h. to bring Edna back to 1931.
Since the timeline of the DeLorean that Edna was driving was overwritten, that DeLorean faded from existence once the time bubble protecting it popped.
Behind the scenes
- Interestingly, the game files contain multiple, identical images of the flux override item. However, given that you can only have one in your inventory at a time, it seems strange that Telltale would waste space creating duplicate textures.