diff --git a/src/bbcode.jl b/src/bbcode.jl
index 1c9b5ae2..aaecae20 100644
--- a/src/bbcode.jl
+++ b/src/bbcode.jl
@@ -371,6 +371,7 @@ const IdToIdDict = Dict{ID,ID}
 function replace_ids(d::IdToIdDict, inst::NewInstruction)
     return NewInstruction(inst; stmt=replace_ids(d, inst.stmt))
 end
+replace_ids(d::IdToIdDict, x::ID) = get(d, x, x)
 function replace_ids(d::IdToIdDict, x::ReturnNode)
     return isdefined(x, :val) ? ReturnNode(get(d, x.val, x.val)) : x
 end
diff --git a/src/refelim.jl b/src/refelim.jl
index 2278afbf..f0eb05fd 100644
--- a/src/refelim.jl
+++ b/src/refelim.jl
@@ -37,14 +37,6 @@ actually needed across boundaries, and eliminates all calls to `set_ref_at!` tha
 to be retained.
 
 Returns a tuple of the modified `BBCode` and the modified `refs` tuple.
-
-!!! note
-    Right now, `eliminate_refs` does not remove dead refs from the `refs` tuple itself (so the 
-    TapedTask will be constructed with the same `refs` tuple as before). We simply leave those
-    refs as unused (i.e., they will be initialised with nothing, and never read from or
-    written to.) In principle, we could also slim down the `refs` tuple itself by removing
-    the dead refs from it. This is left as a future optimisation (and the signature of this
-    function is designed to allow for this in the future).
 """
 function eliminate_refs(ir::BBCode, refs::Tuple)
     # The `refs` tuple contains a series of `Ref`s which are used to maintain function state
@@ -189,21 +181,15 @@ function eliminate_refs(ir::BBCode, refs::Tuple)
     # Only the refs that are live at the end of some basic block anywhere in the function
     # need to be kept. Note that the last ref in `refs` is always mandatory: it's the one
     # that stores the return block (i.e., how far through the function it's progressed).
-    necessary_ref_ids = sort!(collect(union(values(live_out)...)))
-    unnecessary_ref_ids = setdiff(1:(length(refs) - 1), necessary_ref_ids)
+    necessary_ref_ids = sort!(vcat(length(refs), collect(union(values(live_out)...))))
+    unnecessary_ref_ids = setdiff(1:length(refs), necessary_ref_ids)
 
-    # TODO(penelopeysm): We could reduce the size of the ref tuple itself, by dropping refs
-    # that are never used. I think this is not super important right now: it doesn't really
-    # hurt to have extra refs lying around in the tuple, because they're just initialised to
-    # essentially null pointers and never read/written to. But in principle we could get rid
-    # of them too.
-    #
-    # new_refs = tuple(
-    #     [ref for (i, ref) in enumerate(refs) if !(i in unnecessary_ref_ids)]...
-    # )
-    # refid_to_new_refid_map = Dict{Int,Int}(
-    #     necessary_ref_ids[i] => i for i in eachindex(necessary_ref_ids)
-    # )
+    new_refs = map(i -> refs[i], tuple(necessary_ref_ids...))
+    # Suppose that we want to keep refs 1, 4, and 5. Then this map would be Dict(1 => 1, 4
+    # => 2, 5 => 3).
+    refid_to_new_refid_map = Dict{Int,Int}(
+        refid => i for (i, refid) in enumerate(necessary_ref_ids)
+    )
 
     # We now need to go through the IR and remove calls that get/set the unnecessary refs.
     new_bblocks = map(ir.blocks) do block
@@ -263,8 +249,14 @@ function eliminate_refs(ir::BBCode, refs::Tuple)
                         else
                             error("Unexpected value argument to set_ref_at!: $value_arg")
                         end
-                        ninst = replace_ids(old_ssaid_to_new_ssaid_map, inst)
-                        push!(new_insts, (id, ninst))
+                        ninst = Expr(
+                            :call,
+                            Libtask.set_ref_at!,
+                            replace_ids(old_ssaid_to_new_ssaid_map, inst.stmt.args[2]),
+                            refid_to_new_refid_map[refid],
+                            replace_ids(old_ssaid_to_new_ssaid_map, inst.stmt.args[4]),
+                        )
+                        push!(new_insts, (id, new_inst(ninst)))
                     end
                 elseif call_func == Libtask.get_ref_at
                     refid = inst.stmt.args[3]
@@ -279,16 +271,44 @@ function eliminate_refs(ir::BBCode, refs::Tuple)
                         old_ssaid_to_new_ssaid_map[id] = refid_to_ssaid_map[refid]
                     else
                         # It's a get that we legitimately still need.
-                        ninst = replace_ids(old_ssaid_to_new_ssaid_map, inst)
-                        push!(new_insts, (id, ninst))
+                        ninst = Expr(
+                            :call,
+                            Libtask.get_ref_at,
+                            replace_ids(old_ssaid_to_new_ssaid_map, inst.stmt.args[2]),
+                            refid_to_new_refid_map[refid],
+                        )
+                        push!(new_insts, (id, new_inst(ninst)))
                     end
                 else
                     # Some other call instruction.
                     ninst = replace_ids(old_ssaid_to_new_ssaid_map, inst)
                     push!(new_insts, (id, ninst))
                 end
+            elseif inst.stmt isa IDPhiNode
+                # Replace any SSA IDs in the phi node.
+                ninst = replace_ids(old_ssaid_to_new_ssaid_map, inst)
+                # then replace any TupleRefs with the new ref id
+                new_values = Vector{Any}(undef, length(ninst.stmt.values))
+                for n in eachindex(ninst.stmt.values)
+                    if isassigned(ninst.stmt.values, n)
+                        val = ninst.stmt.values[n]
+                        new_values[n] = if val isa Libtask.TupleRef
+                            if !haskey(refid_to_new_refid_map, val.n)
+                                # This should never happen, because if `val.n` was in the
+                                # phi node, it always counts as an upwards-exposed use of
+                                # that ref, and should therefore always be included in
+                                # `necessary_ref_ids`.
+                                error("found TupleRef with unused ref id $(val.n)")
+                            end
+                            TupleRef(refid_to_new_refid_map[val.n])
+                        else
+                            val
+                        end
+                    end
+                end
+                push!(new_insts, (id, new_inst(IDPhiNode(ninst.stmt.edges, new_values))))
             else
-                # Some other (non-call) instruction.
+                # Some other (non-call, non-PhiNode) instruction.
                 ninst = replace_ids(old_ssaid_to_new_ssaid_map, inst)
                 push!(new_insts, (id, ninst))
             end
@@ -296,13 +316,18 @@ function eliminate_refs(ir::BBCode, refs::Tuple)
         return BBlock(block.id, new_insts)
     end
 
+    # The tuple of refs is passed in as the first argument to the IR, so we need to update
+    # the types.
+    new_argtypes = vcat(typeof(new_refs), copy(ir.argtypes[2:end]))
+
     new_ir = @static if VERSION >= v"1.12-"
-        BBCode(new_bblocks, ir.argtypes, ir.sptypes, ir.debuginfo, ir.meta, ir.valid_worlds)
+        BBCode(
+            new_bblocks, new_argtypes, ir.sptypes, ir.debuginfo, ir.meta, ir.valid_worlds
+        )
     else
-        BBCode(new_bblocks, ir.argtypes, ir.sptypes, ir.linetable, ir.meta)
+        BBCode(new_bblocks, new_argtypes, ir.sptypes, ir.linetable, ir.meta)
     end
-    # return ir, refs
-    return new_ir, refs
+    return new_ir, new_refs
 end
 
 # Return a vector of block IDs in reverse postorder on the reverse CFG (i.e., the CFG where
diff --git a/src/test_utils.jl b/src/test_utils.jl
index 98e3abc0..9285cfc5 100644
--- a/src/test_utils.jl
+++ b/src/test_utils.jl
@@ -226,7 +226,7 @@ function test_cases()
             "default kwarg tester", nothing, (default_kwarg_tester, 4.0), (;), [], allocs
         ),
         Testcase(
-            "final statment produce",
+            "final statement produce",
             nothing,
             (final_statement_produce,),
             nothing,