Fix calculation error after form has been submitted

OK, you need to create two Actions, then. One to export the form data to an FDF file, and one to fix the code and then import it back in.
This is the code to use for the first Action:

this.exportAsFDF({bAllFields: true, cPath: this.path.replace(/\.pdf$/i, ".fdf")});

This is the code for the second Action:

var newCalcCode = "\
var v1 = AFMakeNumber(getField(\"Total A1\").value);\n\
var v2 = AFMakeNumber(getField(\"Total A2\").value);\n\
var v3 = AFMakeNumber(getField(\"Total A3\").value);\n\
var v4 = AFMakeNumber(getField(\"Total B1\").value);\n\
var v5 = AFMakeNumber(getField(\"Total B2\").value);\n\
var v6 = AFMakeNumber(getField(\"Total B3\").value);\n\
event.value= (v1+v2+v3+v4+v5+v6);";
this.getField("Total points allocated for Functionality").setAction("Calculate", newCalcCode);
this.importAnFDF({cPath: this.path.replace(/\.pdf$/i, ".fdf")});
this.calculateNow();

You also need to add a Save command to this Action, after executing the code.

Now run the first Action on all of your original files, then the second one. That part might be a bit tricky as Acrobat attempts to process all non-PDF files, unfortunately, so you might have to select them manually, instead of just selecting the entire folder (since it will also contain the new FDF files we created in the previous Action).

Edit: code fixed