Resources should be versioned and old resource files available at specific URLs. There can also be a URL to access the "latest" version. HTML files for ontologies, etc. should indicate the version and have a change log.
Even minor bug-fixes should be versioned, and the most specific link to a resource should refer to a "write-only" file that is guaranteed not to change.
Semantic versioning can be used, e.g. 1.0.1.
To discuss...
See also w3c/wot-discovery#535