When I tried to deploy data/ERAIN_SFC12_MM@9e7c31aba58befc9d02d8a2945e95ad5977820f8 (which moves files around) into the existing .../v1.x.x/, the following happened:

Error updating the git index:
error: data/grb/ERAIN_SFC12_MM_10SI_207_1-456.grb: cannot add to the index - missing --add option?
fatal: Unable to process path data/grb/ERAIN_SFC12_MM_10SI_207_1-456.grb

Removing the worktree, leaving .bare/ERAIN_SFC12_MM/ untouched, and re-deploying worked fine.