This happens when you farm, for example, those 3 convicts and at some point just quit the game. What happens during the farm is that the game counts those eaten brains, reports them to Steam (this is why Steam counter changes, although it may (and very often does) update in portions), but when you quit, the game never saves this number to your local save file. Say, you've completed the game and ate 500 brains, and have this number in your save file. You start farming, farmed another 300 brains using those 3 poor convicts. Steam shows 800, but the game didn't save this number to your drive. Now you quit and the file still has 500. Next time you start farming, you will start from 500! Again!

Don't try to edit the save file! You will just ruin it. And if you are stubborn and want to try to edit it anyway, at least make a backup first!

When you decide to stop farming, just walk forward until the game tells you it has been saved. Now you are free to quit.
You can also check what number is saved in your save file. The file is stored here:
Open some hex editor[hexed.it] and drag-n-drop file there. On the right there is «Go to», your address is:
Now look at the left side, «32-bit integer». This is your value.

If you want to support me, check out my games!

https://cs2bus.com/steamstore/app/1485900/Eye_caramba/
https://cs2bus.com/steamstore/app/682780/Breaking_Good/