User wants to add only VAT on the project invoices. So the user updated MST in Global Settings > Taxes and kept the item taxes (Tax 1/2/3) blank. Are the updated taxes going to be applied to existing time entries?
Any changes you make to the MST and MST(E) fields in Global Settings only apply to new clients by default, not to existing ones. Core prompts you to update existing clients and projects with the new taxes. If you want to apply the new tax rates to your existing projects and clients, choose Yes. Similarly, the rates you specify at the client level only apply to new projects of the client. The rates at the project level always take precedence. Check the Core Help for details. Also check out this article: Taxes in Core.
For the item taxes (Tax 1/2/3 for activity and expense items), the rates you specify in Global Settings apply to new activity and expense items that you create. To update these rates for existing entries, you can use the Batch Update option in Time Entries and Expense Entries. Check the Core Help for details.