I am not sure if those files will be replaced during upgrade, but I have the following content in both of those files.
The /home/yellowtent/boxdata/custom_pages/app_not_responding.html is safe and won't be replaced. But the splash page will get replaced.
I think there is a bug/unintended side effect of the change I made. I will look into fixing it. I guess splash.html is really notfound.html and this can be branded as one needs. I created https://git.cloudron.io/cloudron/box/-/issues/755