That is the reason why I use several different user accounts. Most of them are only for testing purposes for forum requests on issue XYZ on version ABC, but I have one account only for creating bundles.
This account is cleared from its resources before I begin creating a new bundle, and after clearing, I copy those things into that account that I like to bundle. Furthermore, I have deleted all the resources Krita can bundle from Krita’s installation directory of that account. This setup lets me use my standard installation all the time, without the need to change anything on it.
Also, it enables me to have more than one Krita running at the same time. That is very handy, for instance when you run into an issue while bundling, and you need to create or manipulate a resource for the bundle you are working on, but with a resource that is not in the bundle you create, then I don’t need to revert my Krita like it would be with @RamonM’s approach, I just open the other Krita and am ready to do whatever is needed, and when that manipulation is done I copy it back over.
Another advantage is that you can run all installations from one account, you don’t need to constantly log off and log on back and forth, because you can run every software from one account under a different user via runas using Windows. And Linux or macOS offer similar ways to run a software with different rights, that is no issue or obstacle.
Once I showed how this works, and it sounds more difficult to set up as it is:
Michelist