How to use each replacement only once in a list of replacements

One way is to use the following:

GeneralUtilities`ListIterator
GeneralUtilities`IteratorExhausted

Then it can be done with Replace or ReplaceAll:

Needs@"GeneralUtilities`"

Module[{hold},
  SetAttributes[hold, HoldAll];
  
  oneTimeRules[rules_] :=
   
   Normal@Merge[rules, ListIterator] /. Rule -> RuleDelayed /. 
     i_GeneralUtilities`Iterator :> 
      With[{r = Read[i]}, hold[r, r =!= IteratorExhausted]] /. 
    hold -> Condition;
  
  ];

Example:

Replace[{a, b, a, a, b, b}, oneTimeRules@{a -> 1, a -> 2, b -> 3}, 1]

(*  {1, 3, 2, a, b, b}  *)

It does not work with patterns:

Replace[{a, b, a, a, b, b}, 
 oneTimeRules@{x_ -> f[x], x_ -> 2, b -> 3}, 1]

(* {f[x], 2, a, a, 3, b}  <-- should be f[a] *)

---

Addendum

I thought this modification of @Nasser's approach (now deleted), derived from , seemed a better idea. It seems to work with patterns.

ClearAll[useOnce, useRepeated];
SetAttributes[useRepeated, Listable];
useRepeated[(Rule | RuleDelayed)[pat_, repl_], n_ : 1] :=
  Module[{used = 0},
   pat :> repl /; used++ < n
   ];
useOnce[r_] := useRepeated[r];

Replace[{a, b, a, a, b, b}, useOnce@{a -> 1, a -> 2, b -> 3}, 1]
(*  {1, 3, 2, a, b, b}  *)

Replace[{a, b, a, a, b, b}, useOnce@{x_ -> f[x], x_ -> 2 x, b -> 3}, 1]
(*  {f[a], 2 b, a, a, 3, b}  *)

The function useRepeated lets a rule be applied up to n times, by default 1. The function useOnce is shorthand useRepeated with n = 1. The *Iterator family uses similar internal data to keep track of where an Iterator is, so if I were using this, I'd prefer useOnce.

This uses FirstPosition and ReplacePart. It works on the OP's example, not sure how extensible it is.

replaceOnceOnly[expr_, rules_] := Module[{val = expr, part},
    Function[
        If[Not[MissingQ[part = FirstPosition[val, #]]],
            val = ReplacePart[val, part -> #2]
        ]
    ]@@@rules;
    val
];
In[14]:= replaceOnceOnly[{a, b, a}, {a -> 1, a -> 2, b -> 3}]

Out[14]= {1, 3, 2}

Here a solution which will adjust the behaviour of a set of rules which contains "duplicate" rules:

adjust[strategy_, rules_] :=
  Hold@@@GatherBy[rules, First] //
  Map[With[{vs = #[[All, 2]]}, strategy[RuleDelayed@@{#[[1, 1]], Unevaluated@vs}]]&]

cycle[k_ :> vs_] := Module[{i = 0}, k :> vs[[1+Mod[i++, Length@vs]]]]
oneshot[k_ :> vs_] := Module[{i = 0}, k :> Module[{ii = ++i}, vs[[ii]] /; ii <= Length[vs]]]
padlast[k_ :> vs_] := Module[{i = 0}, k :> vs[[Min[++i, Length[vs]]]]]
normal[k_ :> _[v_, ___]] := k :> v

Multiple Strategies

The various strategies are...

... cycle which cycles through the rules repeatedly:

{a, b, a, b, b, b, a, a} /. adjust[cycle, {a -> 1, a -> 2, b -> 3}]

(* {1, 3, 2, 3, 3, 3, 1, 2} *)

... padlast which reuses the last rule as "padding":

{a, b, a, b, b, b, a, a} /. adjust[padlast, {a -> 1, a -> 2, b -> 3}]

(* {1, 3, 2, 3, 3, 3, 2, 2} *)

... oneshot which just lets the rules run out:

{a, b, a, b, b, b, a, a} /. adjust[oneshot, {a -> 1, a -> 2, b -> 3}]

(* {1, 3, 2, b, b, b, a, a} *)

... and normal which is the regular behaviour where extra "duplicates" are ignored:

{a, b, a, b, b, b, a, a} /. adjust[normal, {a -> 1, a -> 2, b -> 3}]

(* {1, 3, 1, 3, 3, 3, 1, 1} *)

RuleDelayed Replacements

The solution also supports replacements that use RuleDelayed (:>).

Given:

$rules =
  { f[x_] :> x, f[x_] :> 10x, f[x_] :> 100x
  , g[x_] :> -x, g[x_] :> -10x
  , h[x_] :> Echo["Evaluation Leak!"]
  };

$exprs = {f[1], g[2], f[3], g[4], f[5], f[6], g[7]};

Then:

$exprs /. adjust[cycle, $rules]
(* {1,-2,30,-40,500,6,-7} *)

$exprs /. adjust[oneshot, $rules]
(* {1,-2,30,-40,500,f[6],g[7]} *)

$exprs /. adjust[padlast, $rules]
(* {1,-2,30,-40,500,600,-70} *)

$exprs /. adjust[normal, $rules]
(* {1,-2,3,-4,5,6,-7} *)

Limited Support for Condition

Beware that the exhibited implementation only supports Condition (/;) on the left-hand side of a rule:

Range[10] /.
  adjust[cycle, {x_ /; x < 7 :> "small", x_ /; x < 7 :> "little"}]

(* {small,little,small,little,small,little,7,8,9,10} *)

It does not support conditions on the right-hand side, whether "bare" or nested within a scoping construct:

1 /. adjust[cycle, {x_ :> "small" /; x < 7}]

(* incorrect result:   small /; 1 < 7 *)