you should be able to keep your save and transfer it to the new download! just go into your current files and find the file thats called "Save01" (or whichever number save you wanna keep), drag that file onto your desktop (or place you can keep track of it), then delete the other files, redownload the game and after you install it just drag that save file over into the folder and you should be able to load it up from there!
im sorry for the trouble! im not sure why you cant save at save points ;-; i havent heard anyone else getting this issue, just to make sure though, this save file isnt from an older version of the game right? if it is from an older build of the game, it can mess it up because you USED to be able to save from menu, but thats since been removed and if you were to try to save from menu with an old build save it would probably mess up O:
and no worries! hope this fixes it!