Anything is possible with VB.NET. You could even edit the machine code contained in an executable if you wanted. Of course, if you don't know the exact binary format of the executable and replace it with something meaningful then the new file simply won't run. The same goes for an FLV file. If you understand the format and can write VB code to parse it and write something meaningful back then you can do what you want.

Generally, for things like this a small number of people will write components to specifically read and write files of a particular format and then everyone else includes one of those components into their applications. You could see if such a component exists for FLV files that can be incorporated into a .NET app.