dir=SetDirectory["C:\\drorbn\\AcademicPensieve\\2016-03"]

nb=Get["SnG.nb"]

Cases[nb, "ϵ", ∞] // Length

Cases[nb, SubscriptBox["ϵ",_], ∞]

Clear[new];
k=0;
nb1 = nb /. SubscriptBox["ϵ",j_] :> If[Head[new[j]]===String,
SubscriptBox["ϵ",new[j]],
SubscriptBox["ϵ",new[j]=ToString[k++]]
]

Cases[nb1, SubscriptBox["ϵ",_], ∞]

NotebookSave[nb1,FileNameJoin[{dir,"SnG.nb"}]]

NotebookSave[
Get["SnG-FixingEpsilons-4.nb"]/. SubscriptBox["ϵ",j_] :> 
SubscriptBox["ϵ",new[j]],
FileNameJoin[{dir,"SnG-FixingEpsilons-4.nb"}]
]