[#12779] Fix auto persistence during database updates

[marquestye]

Part of #12779

Outline of Solution

• Created getCopy methods for various affected entities
• Add tests for unintentional persistence

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[cedricongjh]

hey @marquestye, apologies for being late to review this

I think it would be good to use this opportunity to standardize the update logic for our entities in this PR. Let's place the checking of validity of the entity in the logic layer, while the db layer should handle the entity not found cases, as the db layer should focus on interfacing with the db, while logic layer handles application logic