No they should have worked, unless you did something wrong when you replaced the files for the new build.
All i did was unpacking the folder and dragged it to the area where my old folder was, and it replaced the old files with new ones, without tuching the save file.
Also make sure if you loading the safe file, that you load the save file one, and not the auto save one. Atleast for being sure it should work. Cause i didnt test if autosave or quicksave fails on load.
Also i dont use the itch app, because some games has trouble with using the app.