FLV and MP4 both are multimedia container format.

Comparison can be found @ http://en.wikipedia.org/wiki/Comparison_of_container_formats

Since both container, you can "decontain" it (actually demux is the right term).

Example:

FLV - use FLV Extract from http://www.moitah.net/

Audio quality ? Depend on which audio they contain. FLV mostly contain AAC.

Sometime I do demux FLV and mux back to MP4, for playbility (as per Bremaine post before).