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.