The saves should be entierly compatible. On most systems they are stored in App data and automatically transfer between game versions. If they aren't for you, then you can manually move the saves from the save file in the old version to the new version.
I ended up doing this, and I can confirm that it works. Only problem it causes is that the desktop itch.io program shows 2 of each launching option. Worked by selecting the second, as I figured despite identical naming, it would be sorted that way. Have not tried to select the first one to see if both route to the newest version.