filter matrix blocks by multiple light switch value, and then merge them
Keep in mind objects in PHP are always called by reference not by value thus your anchors query will always return blocks from the type subhead with the field value anchor =1 while your matrix query anchorLinks will return blocks of type copy with the field value anchor = 1 and anchorLink = 1

I'm not sure why you don't fetch the results in one single query as it would be faster and easier in my opinion but you want to create 2 queries you need to either reset the previously set property to null or use the clone  function 

{% set anchors2 = clone(entry.pageBuilder).type('copy').anchorLink('1').all() %}
{% set anchors1 = clone(entry.pageBuilder).type('subhead').anchor('1').all() %}