The difference between the two flash formats SWF and FLV is the purpose each is developed for.
SWF - ShockWave Flash: used for flash animations which is the most common resulting format when exporting flash projects to it's final product, much like indd (InDesign Document) results in a PDF when exporting from Adobe InDesign.
FLV - Flash Video: a video file encoded to be compatible with flash player and usually used for streaming media/video on networks/internet.
