We only run every night the process PRC: Update Project Summary Amounts, for all projects. That process know to add only the incremental transactions added since last run and only process new or updated commitments.
This process is scheduled to run after all Costing processes are completed.
The process - PRC: Refresh Project Summary Amounts - actually built from scratch the summarization of all transactions and commitments. Therefore this process may take more and more time to complete as your project data is increasing. You should be running this process once after migrating data from legacy system, or if you found an issue with current summarization. Note that could be due to changes you may be doing with Reporting Periods set up not in the right order (period after period, never go back).