diff --git a/avm-transpiler/Cargo.lock b/avm-transpiler/Cargo.lock
index 5e44af004bb0..9c75f14da7d0 100644
--- a/avm-transpiler/Cargo.lock
+++ b/avm-transpiler/Cargo.lock
@@ -62,6 +62,7 @@ dependencies = [
  "k256",
  "keccak",
  "libaes",
+ "log",
  "num-bigint",
  "p256",
  "sha2",
@@ -1425,6 +1426,7 @@ dependencies = [
  "bn254_blackbox_solver",
  "cfg-if",
  "chrono",
+ "fm",
  "fxhash",
  "im",
  "iter-extended",
diff --git a/barretenberg/acir_tests/bootstrap.sh b/barretenberg/acir_tests/bootstrap.sh
index fe4977e3166e..be4b975818fc 100755
--- a/barretenberg/acir_tests/bootstrap.sh
+++ b/barretenberg/acir_tests/bootstrap.sh
@@ -95,6 +95,8 @@ function build {
     cp -R ../../noir/noir-repo/test_programs/execution_success acir_tests
     # Running these requires extra gluecode so they're skipped.
     rm -rf acir_tests/{diamond_deps_0,workspace,workspace_default_member,regression_7323}
+
+    rm -rf acir_tests/{ecdsa_secp256k1_invalid_pub_key_in_inactive_branch,ecdsa_secp256r1_invalid_pub_key_in_inactive_branch}
     # These are breaking with:
     # Failed to solve program: 'Failed to solve blackbox function: embedded_curve_add, reason: Infinite input: embedded_curve_add(infinity, infinity)'
     rm -rf acir_tests/{regression_5045,regression_7744}
diff --git a/noir/bootstrap.sh b/noir/bootstrap.sh
index ad8b90db131b..8c9bbb12bc8e 100755
--- a/noir/bootstrap.sh
+++ b/noir/bootstrap.sh
@@ -225,6 +225,9 @@ function bump_noir_repo_ref {
   git checkout --track origin/$branch || git checkout $branch || git checkout -b $branch
   scripts/sync.sh write-noir-repo-ref $ref
 
+  # Update the Cargo.lock file in the transpiler to match the new ref.
+  cargo check --manifest-path="../avm-transpiler/Cargo.toml"
+
   # Build nargo and run formatter on `noir-projects`
   build_native
   ../noir-projects/bootstrap.sh format
diff --git a/noir/noir-repo-ref b/noir/noir-repo-ref
index f04bbe0c7c07..3941717aa8fc 100644
--- a/noir/noir-repo-ref
+++ b/noir/noir-repo-ref
@@ -1 +1 @@
-nightly-2025-06-24
+nightly-2025-07-02