Timeout issue when updating Opportunities

I have a custom object called "Sales targets" this is for tracking the sales of bussiness. The Sales targets id should be updated in related opportunities (one to many) based on region and  Business unit. We are getting a timeout when updating the opportunities due to the volume of related opportunities against a target.  

Is there any solution for this, like updating the opportunities in batches , incremental jobs, Custom tables to store the updated data to exclude when selecting the opportunities for updating etc.