Since it sounds like new users my want to know what is being copied, I have a suggestion for balancing functionality for seasoned and new users.

Let the pop-up warning appear, but with an option radio button to turn it off. Or at least an admin function to turn it off/on for different users. This will be a spot gap for new users but can be turned on or off by an environmental admin if the user needs it or not.
To improve functionality, either in user settings by security or as an option as an addition to the Copy Invoice feature, give users the option to select which features of the invoice they want to copy. This way if they want to copy distributions, description, but not post date or amount to avoid duplications, they can. This can be accomplished by radio buttons underneath or a button below each "Copy Invoice" section or Copy Options.

Lastly, please combine the old function and the new if possible. Have the old search feature, but also a button if users want to have an expanded search functionality for coping invoices.