That's why MODX refreshes the whole cache by default when you save a resource.
CacheMaster has no way of knowing which chunks need the cache refreshed, so there's no way it can do that.
You can make the chunk tag uncached. That should force it to be processed on every page load (though it will slow things down):
It might be better, though to replace the chunk tag with what's in the chunk and just call the pdoResources snippet uncached.
You can also manually check the empty cache checkbox when you save a resource or clear the cache manually from the Site manu.