User is trying to Batch Update a project for a set of time entries, but their rates do not update based on the associated fee schedule.
This is the expected behavior in Core. If you Batch Update the project, employee, activity or overtime flag on time entries, their rates do not update. You need to update them separately using the Update Rates option. Check the Core Help for details on updating rates.
Note: If you have to change the project, activity, employee or overtime flag on very few entries, you can do it one by one from the Time Entries screen. This also changes the rates for them.