If you are using Time Management to track actuals, in the Cost and Effort policy, you can select the level (task or project) at which actuals are tracked.
If actuals are tracked at the project level, these actuals are not sent to Microsoft Project because Microsoft Project only tracks actuals at the task level. Project level actuals in Microsoft Project are automatically calculated or rolled up from task level actuals.
When you track actuals using Time Management, you can change the level at which actuals are tracked. If you have entered actuals at the task level and then change the project to track time at the project level, you cannot change the level back to the task level until you remove all the actuals for the project from the time sheets that track time against the project.