For that scenario, you will need to make a single Init.bnk file that you will provide as a an update/patch to your game main code for all of your users. This will be the new Init.bnk that supports all DLC available. It is basically a cummulative Init.bnk. Each time you release a new DLC, you will need to provide an update will the new version of Init.bnk.
Then, each of the DLC will contain its own bnk files (but not the Init.bnk) that can be added independently, and each DLC will need to depend on the Init.bnk to be at the correct version.