Maybe you started out using the WORM backend, and have now configured git-annex to use SHA1. But files you added to the annex before still use the WORM backend. There is a simple command that can migrate that data: # git annex migrate my_cool_big_file migrate my_cool_big_file (checksum...) ok You can only migrate files whose content is currently available. Other files will be skipped. After migrating a file to a new backend, the old content in the old backend will still be present. That is necessary because multiple files can point to the same content. The `git annex unused` subcommand can be used to clear up that detritus later. Note that hard links are used, to avoid wasting disk space.