I originally thought this was just from porting over too many variables at once (and it still can be, in which case you just need to copy over the "VariablesData" part twice,) but I've found that getting rid of variables without replacing them with a new value also does this, and the game assigns a new variable to track if your save is from before or after I added in this transfer method, so it can run an important function after you load into your updated save.
The important part is that when you are copying VariablesData, you need to not replace the part that reads "1132":1.0} in your new save. Instead, change this to "1132":0.0} So you'd copy all of your variables from the old save, but only replace up until the last variable (1132) in the new save. You may also need to add a comma after the variable that shows up right before "1132":1.0} Sorry for how confusing this is, I've updated the guide now to include that part.