ediff-autostore-merges is a variable defined in `ediff-init.el'.
Its value is

  • Automatically becomes buffer-local when set.

Save the results of merge jobs automatically.
With value nil, don't save automatically. With value t, always
save. Anything else means save automatically only if the merge
job is part of a group of jobs, such as `ediff-merge-directory'
or `ediff-merge-directory-revisions'.

You can customize this variable.