This is on the Back Office > Survey > Processes > Orders > Manual Invoices Page.
The message appears when 'Additional Items' is selected and the 'Display' button is clicked.
The warning exists to stop you creating or using the additional items for orders that provide system functionality.
If you use 'Additional Items' for purchases such as WIT, MC³ and Surveys, the client will not be given access to them. These should instead be purchased using one of the other buttons.
This is explained further in the following article:
Note: This warning can be ignored if the item published does not assign any functionality across to a company e.g. if the company is asking us to merge their employment groups.