That also depends upon the mod, as to where the animation is stored. Generally, it is in the 3D model for the flag itself, below the texture files, and has to be Exported before the "frames" can been "seen". Notice that in SH4, the "controller" is below the object that is controlled... which is about how the whole game is "built" - upside down and backwards
... There are more than one "flag" file in some mods. Another little "weird" aspect is it almost doesn't matter where something is stored in the game, whether neatly tucked away in specific files in specific folders, or a hodge-podge of bits and pieces scattered about the folder structure. So be sure you are noodling with the correct "part" so that you get what you want.
