Convert F4V to MP4
F4V was Adobe's H.264 answer to the older FLV - an MP4-family container with a different extension. The streams inside (H.264 video, AAC audio) are exactly what MP4 accepts. Wave rewrites the container header and calls it done.
What actually changes
When Adobe added H.264 support to Flash in 2007, it defined F4V as a nearly-verbatim implementation of the ISO Base Media File Format - the same standard MP4 is built on. An F4V file and an MP4 file with the same H.264 + AAC contents are byte-similar to a level a hex editor can walk through side by side. Only the ftyp box and a handful of Adobe-specific atoms differ.
Conversion is a container header rewrite: Wave replaces the F4V ftyp with an MP4 ftyp, moves the moov atom to the start of the file for fast-start playback, and drops the handful of Adobe-only atoms that generic MP4 players ignore anyway. The video and audio streams are copied bit-for-bit. No re-encode, no quality loss.
Three steps.
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Step 1
Drop the .f4v file onto the card.
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Step 2
Wave shows Fast copy - the streams are already MP4-compatible.
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Step 3
Convert and save the MP4.
Answers, specifically.
Why does F4V exist at all if it's basically MP4?
Adobe wanted the Flash Player to distinguish between the older FLV format (VP6 / Sorenson) and the newer H.264 pipeline. Using .f4v made the decoder path unambiguous. Once Flash disappeared, so did the reason for the separate extension.
Is my F4V protected?
Some F4V files from Adobe Access / Flash Access carry DRM (used by BBC iPlayer downloads pre-2015 and various pay-TV catch-up services). Wave can't decrypt those. Unprotected F4V - the vast majority - converts cleanly.
Will my MP4 include the F4V cue points?
Adobe cue points are a Flash-specific construct with no direct MP4 equivalent. Wave drops them. Standard MP4 chapter atoms are preserved when present.
What about audio-only F4A files?
F4A is Adobe's audio-only variant, roughly equivalent to M4A. Wave's scope is video → MP4 (and video → MP3), so audio-only F4A files are refused up front. Rename to .m4a and any player will handle it directly.
Why does the MP4 sometimes seek smoother than the F4V did?
Wave rewrites the moov atom to the head of the file. Some F4V exports left it at the tail, which forces a player to scan the whole file before it can seek to a specific timestamp. A properly front-loaded MP4 seeks instantly.