Depending on what 'flash' your car currently has, it either updates your ECU to the most current telemetry, or it helps your ECU 're-learn' the telemetry it currently has. Yes, it is worth it...especially if there is a new flash available for your Focus. Another variation on 'flash' is a 'tune', which is basically a custom flash which is downloaded into your ECU to improve your engine performance in numerous areas.
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As racer1735 says, it's the program put into your chip that manages all engine functions: ignition & valve timing, fuel injection and for the SVT, the variable intake manifold. Reflash ususaly refers the the programs written by Ford. RL6 and YFRO are the more recent ones I've heard of, and yes they made a big difference in the way the SVT performed. YFRO got the intake runners to open at 5K vs 6K in the previous tune. Far better than these are what 1turbofocus is refering to. These are usualy called a custom tune and his is a very popular one...and the price he's offering is a real bargain. Go take a look at the tread at the top of this forum called SVT owners: Post reviews of your Tune!