If you don't mind manually editing the file each time, you can comment out line 752 of cp2_vars.cgi:
$problems .= &SetVarsGraemlins;
That will prevent vars_graemlins from ever being written, even if changes are made to the page.
Technically, the file isn't reverted... the stock graemlins are hard-coded in the subroutine, then any changes you've made to the stock set are ported over.
Your particular problem is that you've combined both the stock set and the custom set into just the stock's area, which caused all sorts of problems....
