I’m currently using a similar style of project structure and just copying it over each day. That means that in each subdirectory for each day there is:
day01
├── dune-project
├── dune
├── .ocamlformat
├── lib.ml
├── bin.ml
day02
├── ...
This nicely means that each subdirectory is in some sense its own separate project which feels about right from a philosophical direction. Unfortunately this means that any utilities written end up accumulating over the days in the lib.ml file but otherwise is fine 
.