You can use a magnet or ipfs uri or add a triple that specifies other properties of the file that let you find it.
Semantic web uses IRIs in triples. They serve as identifiers, not locators (URL). This is because semantic web talks about more than just files.
The Web Annotation spec talks about web resources which should be dereferencable. That is a naive assumption that makes the approach brittle. But one can annotate 'sourceDate' and 'cached' which indicate the date for the annotated version and a location for a copy.
When you're annotation a resource it's best to also store a copy. The Web Annotations specification allows this.
