Do Centro de Tecnologia F4V / FLV da Adobe :
As the de facto standard for dynamic media on the web, Adobe Flash supports a number of media formats. These include two core open container formats for delivering synchronized audio and video streams: F4V and FLV. F4V builds on the open standard ISO/IEC 14496-12:2008 (MPEG-4 Part 12) ISO base media file format and supports H.264/AAC–based content. It has a flexible structure and defines specific supported codecs and extensions, facilitating simplified interoperability across tools, services, and clients. FLV supports codecs such as Sorensen Spark and On2 VP6, and encodes synchronized audio and video streams in the same way as they are encoded in SWF files.
Portanto, os dois formatos são distintos.
Outro artigo útil é: Qual é a diferença entre Flash Video (FLV), F4V e H. 264 .