It's a glitch with the mod tool. What's happening is that it's allowing the reimporting of over sized files, therefore once you start the game with your mod everything from that file will disappear. Now there is another glitch with the tools you should keep in mind while you mod, not all files that are extracted can be modified (for example the weapon files). So before you start modding, make a new folder in "bundles" and copy all the files that you want to mod into the new folder*, then reimport one file at a time, start the game and if everything from that file is still there, then it's ok to mod that file. However, there are some files that can only be modified very lightly. *you don't need to do this, but it does make it easier on you if anything goes wrong