PPO does not overwrite project plans
When a project plan is re-imported into PPO, PPO compares the information in its database with that provided by MSP and updates the Tasks accordingly. PPO does not overwrite the Tasks in the Tasks section, it finds the correct Task in PPO and updates it. The following article explains in detail the mechanisms and rules involved.
The Unique ID field in MSP
In order for PPO to know which Task to update with which information from Microsoft Project (MSP), PPO makes use of MSP's Unique ID field. Each task in MSP has a unique ID, which can be viewed by implementing the Unique ID field on your MSP plan.

When you import your project plan into PPO for the first time, the Unique ID is imported into PPO and saved in the Task Code field along with the PPO project key for the project. The Task Code field is hidden (cannot be seen by users from the front end) but can be used by the PPO Support Team for investigation during support calls.
What happens when you re-import?
When you re-import your project plan, PPO maps each task in the PPO Tasks section to the tasks provided in the MSP project plan by using each Tasks Unique ID (as described above). When PPO finds matching Unique ID's it updates the Task in PPO with the information from MSP.
This mechanism ensures that the correct Task is updated, even though a project plan may contain more than one Task with the same name.