In the settings menu there is an option for Primavera P6 to use activity IDs for synchronization. The same option for Synchro .sp files (and other formats) would be very useful as synchronization from external data goes through GUIDs by default. But, when you update schedule all links between tasks in previous version of this schedule and parts of different schedules in this project are deleted same as 3D resources assighnments. New schedule has the same task IDs, but different GUIDs, so the links are not saved after synchronization.
Thank you for submitting this idea. Unfortunately we will not consider it at this time. We will re-consider it in the future when it is possible. We value your feedback and thank you again!