1.) Go to this location on your PC:
C:\Users\[YourName]\AppData\Local\SN1
(replace the [YourName] with the name of your Windows profile name)
NOTE: The AppData folder is hidden by default, so you might have to make hidden folders visible first!
(https://www.howtogeek.com/howto/windows-vista/show-hidden-files-and-folders-in-windows-vista/)

2.) Right-click the settings file (settings.ini) and open it with Editor.

3.) Change the "Points" value to anything you want. For example, if achievement 100 is missing for you, change it to 99.

4.) Save the file and start the game in Infinite Mode. Once you collect an apple, you should receive your missing achievement.

Alternative: If you're having trouble finding the location, you can also use your Windows Explorer's search function and search for the folder "SN1". This might take a while though, depending on how many files you have saved on your PC.

Hope this helps! If you have any questions, feel free to contact me.