Crankshaft can be updated from the same place you installed it from.
If you installed the Flatpak using a GUI (like KDE Discover or Gnome Software), you should be able to use the same program to update it.
To update the Flatpak from the command line, run:
flatpak update space.crankshaft.Crankshaft
There’s currently an issue where after updating, you may need to
restart the autostart service to start using the new update. To do this, run
systemctl --user restart crankshaft.service.
Alternatively, you can restart your device.