I ran into this problem on my framework laptop (running NixOS): after an upgrade of the system, fprintd suddenly does not work. Checking the logs of the fprintd service suggest that the storage is corrupted. At that moment no fprintd-* command could run successfully, even fprintd-delete was not working.
The solution seems to be force clearing the storage. Thankfully, I found this solution of Shy_Guy from the framework laptop's community, which is in turn based on Kani's script on framework discord.
I put up this small flake to make the procedure slightly simpler just in case it will help the other ones who run into the same problem.
So basically you need to run the script inside a development environment. With this flake, this is as simple as two commands:
$ sudo nix develop "github:nixvital/fprint-clear"
# After entering the environment
$ fprint-clearPlease note that the sudo for the nix develop is very important since the script requires the super user privilege to run.