Sorry, your post is a bit confusing.
Nothing should be lost when purchasing iCloud storage.
iCloud storage only adds storage for iCloud, but does not affect anything else.
If you are using an account for iCloud and one for Media & Purchases, then they are entirely separate and one does not affect the other. Do note, however, that the account used for iCloud will need to have a valid payment method added to it to purchase iCloud, as it will not use the payment methods from the separate Media & purchases account.
With that said, Apple IDs should not be shared for any reason. Each person in the family, including children, should have their own, and if you want to share purchases and subscriptions you can do so through Family Sharing.
This has the added benefit of keeping everybody's content, purchases, media and other data entirely separate from everybody else.
click here ➜ How to set up Family Sharing on your iPhone, iPad, or Mac - Apple Support
If your setup is not this, then please clarify what exactly it looks like as its not clear exactly what the account set up is actually like.