Deleted CloudKit files just re-download

Hello and thanks for getting back to us here in Communities, ScienceTeacher_99.

To confirm, are you using the steps here for deleting the iCloud Messages? Manage your iCloud storage - Apple Support

"Delete texts and attachments in Messages

When you use Messages in iCloud, all of your text messages and the attachments you send and receive use your iCloud storage. You can make more space available when you delete texts and attachments—like photos, videos, and files—that you don't need anymore. 

Mac

To delete a message or attachment, follow these steps:

1. Open a message conversation.
2. Control-click the blank area of a message bubble that you want to delete.
3. Choose Delete.
4. Click Delete.

To delete multiple attachments from a contact or conversation, follow these steps:

1. Open a message conversation.
2. Click the Info button .
3. Scroll to the Photos section.
4. Click on an attachment then hold the Command key to select multiple attachments. 
5. Control-click or right-click, then choose Delete.
6. Click Delete Attachment to confirm. 

To delete an entire conversation, follow these steps:

1. Control-click a conversation.
2. Choose Delete Conversation.
3. Click Delete."

If you've done this exact step to delete messages, how long have you waited before checking? It could take some time for iCloud to reflect the difference. Make sure that you're also connected to a stable internet connection as well.

Per this article, here is what is classified under System Storage: See used and available storage space on your Mac - Apple Support

• "System Data: Contains files that don’t fall into the categories listed here. This category primarily includes files and data used by the system, such as log files, caches, VM files, and other runtime system resources. Also included are temporary files, fonts, app support files, and plug-ins. You can’t manage the contents of this category. The contents are managed by macOS, and the category varies in size depending on the current state of your Mac. You can manage your data that falls outside the other categories using Finder or the 3rd party apps that created it."

Additionally, here's some great information regarding CloudKit:

CloudKit security - Apple Support

CloudKit end-to-end encryption - Apple Support

"Messages in iCloud

Messages in iCloud, which keeps a user’s entire message history updated and available on all devices, also uses CloudKit end-to-end encryption with a CloudKit service key protected by iCloud Keychain syncing. If the user has enabled iCloud Backup, the CloudKit service key used for the Messages in iCloud container is also backed up to iCloud to allow the user to recover their messages, even if they have lost access to iCloud Keychain and their trusted devices. This iCloud service key is rolled whenever the user turns off iCloud Backup."

Do you have other Apple devices using the same Apple ID for Messages?

Keep us updated.

Cheers!

Hello ScienceTeacher_99,

Thanks for asking about CloudKit. How much storage is used in your iCloud storage?

If you delete items in iCloud, be aware that they will also delete from your devices, but reducing your iCloud storage can be done using this article: Manage your iCloud storage - Apple Support

Thanks.