User bills the fixed projects to the clients only two times: one is upfront and then at the end when the projects are complete. Although the user enters time on the projects, it is not used for billing. Are these time entries cleared from Work-in-Progress (WIP) after the billing is done?
It depends on how you bill a fixed project. If you are using manual invoices and not linking the time and expense entries to them, you need to mark the entries as Billed after you are done invoicing to clear them from WIP. On the other hand, if you create the invoices from the Create Batch Invoice screen for a fixed amount by updating the Net Bill or Percent Complete fields, the approved time and expense entries of the projects are linked to the invoices and marked as Billed automatically.
The ideal approach in your case is to link all the time and expense entries on the project to the second invoice, the one you create when the project is complete. First, make sure all the entries that you created during the course of the project are approved. Now, if you want to create a manual invoice at the end, choose the option Approved Time Entry & Expense Entry under Create From in the Create Invoice dialog. Check the Core Help for details. Core attaches the approved entries to the invoice and marks them as billed, clearing the WIP. Otherwise, you can create the invoice from the Create Batch Invoice screen by updating the Net Bill or Percent Complete fields. The approved time entries are automatically attached to it and marked as Billed. Check the Core Help for details.
Note: If you want to avoid linking the entries to the invoices and only clear the WIP, you can simply approve them and batch update their Billed Status flag to True before creating the invoices. The entries are cleared from the WIP, but not linked to any invoices. Check the Core Help for details on that.