I haven't had any problem with lost progress during development, though I know games on itch have had trouble with saves in the past when games were updated. I was able to update this a couple times and it kept my saves... but if you are still worried, play on https://sokoban-notebook.com/ (which will be a stable url for localStorage), or 'export data' from the title screen now and then.
Its a bit tricky at first, yeah, but I have a hard time going back to the usual controls now, ha. I did try animating a little guy that follows your movements, but found it distracting - a bit like there was something stuck to your finger you couldn't get off! Maybe there's a way to make it work, I'll keep it in mind for the future :)
I'm so glad to hear the annotations help! I've really appreciated having them too, for the deductive play style, but also its so nice to be able to pick up where I left off without needing to remember how parts of the solution go, especially on bigger levels.
I've been downloading packs from http://www.sokobano.de/en/levels.php. There's a link to it on the import screen, too.