Seeing that you mention flask I assume you are running carputilsGUI? carputilsGUI is supposed to be a tool for starters to run some of the examples in a web-based environment. Building new ionic models is not supported from the web-based GUI.
If you want to compile new ionic models, then installation from source is the best option: https://opencarp.org/download/installation
As you identified correctly, cellml_converter.py is located in the subfolder physics/limpet/src/python of the openCARP repository. Calling it with the full path will solve the issue. We've added this to the documentation of this example: https://git.opencarp.org/openCARP/experiments/-/commit/b06d51ea12f0688786be800dbf68a9ab2bf13750
A version of the luo_rudy_1994.model file is already shipped with the experiment, that's probably what you see.
Also for limpet_fe.py, you need to provide the full path if the folder \$openCARProot/physics/limpet/src/python is not in your $PATH.