caddux, to be honest, I'm not sure. Until TaleWorlds has settled most of the issues and releases a more or less "final patch" (or at least one that will last a good long while), what I'm doing is adding all my modded content to a new module called "Native Revised". You can do the same thing. Just copy your entire "Native" folder and paste it in the same modules directory. You can name it anything you want. Apply all your mods to THAT module only, and chose to run it from the Warband splash screen. This leaves you with a pristine Native module which is helpful in case you ever mess something up and want to get a file from it.
In any case, like I say, until TaleWorlds settles on a long term patch, I'm just adding my content to my Native Revised mod. When a new patch is released, I make a new "Native Revised" and re-add all my content. Just go ahead, make a new module, add this banner pack to it, and then when a new patch is released, do it all over again. Hopefully they won't take as long to work out all the bugs (as I fear), and we won't have to do this stuff over and over again.
Does anyone have a better answer for this question, or know of any easier way to ensure that our modded content continues to work even when the game is re-patched?