The Toolbar, being a child of the AppBarLayout, gets its LayoutParams from the AppBarLayout. These layout params have the scroll flags that are set in the XML.
So, you get the AppBarLayout.LayoutParams from the Toolbar, and call
setScrollFlags() to change the flags to the value you want.
Toolbar toolbar = findViewById(R.id.toolbar); // or however you need to do it for your code
AppBarLayout.LayoutParams params = (AppBarLayout.LayoutParams) toolbar.getLayoutParams();
params.setScrollFlags(AppBarLayout.LayoutParams.SCROLL_FLAG_NO_SCROLL); // clear all scroll flags