Although you can’t tag a project to a specific line item on an invoice, you can now use the new Project Adjustments feature for apportioning a smaller amount from an invoice to a project.
Say you have an invoice for £100 tagged to a project. If in actual fact only £10 of that sale was attributable to that particular project, you can now enter an adjustment for -90 to revise the project totals.
As I say it doesn’t directly answer the original question but it is a solution in terms of getting the figures where you want them to be. For that reason I will tentatively mark this as Implemented 