why is progress not saved on the itch.io one?
To elaborate on what ISS4C_F0ST3R said, itch.io generates a new temporary website every time I upload new files. Since saves are stored on the website, when a new website is generated it loses the saves on the old website. The only way to fix this is to play on https://rugbug/net/redmatch2 or download the game.
In the next update I am adding in cloud-based user accounts so players can keep data as it will no longer be stored on itch, but on a separate server which will not wipe data when there is an update, so you will be able to play on itch.io again. Until then, I recommend doing one of the two options above.