It depends on which version of vShare are you talking about (2.7 or 2.8 ). The process that you are describing above only exists on your mobile enabled vShare 2.7 site (only a 2.7 with my mobility mod would create two files). In an unmodified 2.7, it is a easier to make this happen (you can change the references in the functions_upload.php from flv to mp4). In an unmodified 2.8, this is possible to do as well by changing the functions that handle flvs and make them mp4 (and, in fact, depending on if you have an early release of the 2.8.1 code or a fixed release, your vShare 2.8 unmodified code could likely be doing this already).
For modified sites (i.e. like the ones that have the mobile mod installed), there is a bit more work to be done, but it is all possible to do by simply modifying your functions_upload.php file to not convert the files.
Also, for the record, one would never start a discussion saying that it won't work because of faststart as faststart really has nothing to do with being able to play back a MP4. The biggest argument one would have about not converting the video has to do with compatibility (and I'm not referring to device capability). A couple of years ago, I wrote an article on this forum about it. I don't remember the exact link, but basically, the issue is that the Abobe Flash Player standard can only playback particular profiles within AVC (MPEG-4 Part 10, which is also known as H.264). AVC is a particular type of MP4 video. The reason why this is an issue is because within the MPEG-4 standard, you actually have 2 parts (of a total of 29, BTW) that deal with video: Part 2 and Part 10. Within both parts are several profiles. Each of these profiles contain various different enhancements, features, etc., but the gist of it is that it can only be certain profiles and features within the Part 10 standard. Most modern day computers can playback all of the profiles and both parts very easily, but Flash can only read specific profiles from a single part. This, in turn, means that a MP4 file (which is just a container) can comprise of different types of videos, some of which are not actually compatible with Flash players.
If you are converting your own videos and are confident that they are within spec for Flash, then no one here is going to (or at least, shouldn't) care to talk you out of doing that. All converting is really doing is ensuring the capability with Flash. Now, if you are also doing this on a site that has the mobile mod installed, the only thing I would caution you on is that you have to remember that mobile devices are more limited than the Flash spec are. Only the most recent of phones (within the last year or two) are capable of playing back anything above a baseline profile. Thus, you will want to ensure that the MP4 file is at a quality and profile level that matches the devices that your users are using.
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