diff --git a/Cargo.lock b/Cargo.lock
index da316c50a..7e30d0c24 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1353,7 +1353,7 @@ dependencies = [
  "iana-time-zone-haiku",
  "js-sys",
  "wasm-bindgen",
- "windows-core",
+ "windows-core 0.51.1",
 ]
 
 [[package]]
@@ -2847,9 +2847,8 @@ dependencies = [
 
 [[package]]
 name = "reflink-copy"
-version = "0.1.11"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f97f7665e51f23760e9e4949d454a4782c76ef954acaeec9d1b0f48a58e4529e"
+version = "0.1.12"
+source = "git+https://github.com/konstin/reflink-copy?rev=1fc25b9ca5087bd20f78546009fe98709e9c4343#1fc25b9ca5087bd20f78546009fe98709e9c4343"
 dependencies = [
  "cfg-if 1.0.0",
  "rustix",
@@ -4176,12 +4175,12 @@ checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f"
 
 [[package]]
 name = "windows"
-version = "0.51.1"
+version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ca229916c5ee38c2f2bc1e9d8f04df975b4bd93f9955dc69fabb5d91270045c9"
+checksum = "e48a53791691ab099e5e2ad123536d0fff50652600abaf43bbf952894110d0be"
 dependencies = [
- "windows-core",
- "windows-targets 0.48.5",
+ "windows-core 0.52.0",
+ "windows-targets 0.52.0",
 ]
 
 [[package]]
@@ -4193,6 +4192,15 @@ dependencies = [
  "windows-targets 0.48.5",
 ]
 
+[[package]]
+name = "windows-core"
+version = "0.52.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "33ab640c8d7e35bf8ba19b884ba838ceb4fba93a4e8c65a9059d08afcfc683d9"
+dependencies = [
+ "windows-targets 0.52.0",
+]
+
 [[package]]
 name = "windows-sys"
 version = "0.45.0"
@@ -4241,6 +4249,21 @@ dependencies = [
  "windows_x86_64_msvc 0.48.5",
 ]
 
+[[package]]
+name = "windows-targets"
+version = "0.52.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8a18201040b24831fbb9e4eb208f8892e1f50a37feb53cc7ff887feb8f50e7cd"
+dependencies = [
+ "windows_aarch64_gnullvm 0.52.0",
+ "windows_aarch64_msvc 0.52.0",
+ "windows_i686_gnu 0.52.0",
+ "windows_i686_msvc 0.52.0",
+ "windows_x86_64_gnu 0.52.0",
+ "windows_x86_64_gnullvm 0.52.0",
+ "windows_x86_64_msvc 0.52.0",
+]
+
 [[package]]
 name = "windows_aarch64_gnullvm"
 version = "0.42.2"
@@ -4253,6 +4276,12 @@ version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8"
 
+[[package]]
+name = "windows_aarch64_gnullvm"
+version = "0.52.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cb7764e35d4db8a7921e09562a0304bf2f93e0a51bfccee0bd0bb0b666b015ea"
+
 [[package]]
 name = "windows_aarch64_msvc"
 version = "0.42.2"
@@ -4265,6 +4294,12 @@ version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc"
 
+[[package]]
+name = "windows_aarch64_msvc"
+version = "0.52.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bbaa0368d4f1d2aaefc55b6fcfee13f41544ddf36801e793edbbfd7d7df075ef"
+
 [[package]]
 name = "windows_i686_gnu"
 version = "0.42.2"
@@ -4277,6 +4312,12 @@ version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e"
 
+[[package]]
+name = "windows_i686_gnu"
+version = "0.52.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a28637cb1fa3560a16915793afb20081aba2c92ee8af57b4d5f28e4b3e7df313"
+
 [[package]]
 name = "windows_i686_msvc"
 version = "0.42.2"
@@ -4289,6 +4330,12 @@ version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406"
 
+[[package]]
+name = "windows_i686_msvc"
+version = "0.52.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ffe5e8e31046ce6230cc7215707b816e339ff4d4d67c65dffa206fd0f7aa7b9a"
+
 [[package]]
 name = "windows_x86_64_gnu"
 version = "0.42.2"
@@ -4301,6 +4348,12 @@ version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e"
 
+[[package]]
+name = "windows_x86_64_gnu"
+version = "0.52.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3d6fa32db2bc4a2f5abeacf2b69f7992cd09dca97498da74a151a3132c26befd"
+
 [[package]]
 name = "windows_x86_64_gnullvm"
 version = "0.42.2"
@@ -4313,6 +4366,12 @@ version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc"
 
+[[package]]
+name = "windows_x86_64_gnullvm"
+version = "0.52.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1a657e1e9d3f514745a572a6846d3c7aa7dbe1658c056ed9c3344c4109a6949e"
+
 [[package]]
 name = "windows_x86_64_msvc"
 version = "0.42.2"
@@ -4325,6 +4384,12 @@ version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538"
 
+[[package]]
+name = "windows_x86_64_msvc"
+version = "0.52.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "dff9641d1cd4be8d1a070daf9e3773c5f67e78b4d9d42263020c057706765c04"
+
 [[package]]
 name = "winnow"
 version = "0.5.19"
diff --git a/Cargo.toml b/Cargo.toml
index 3f95eba3d..6e550cbc4 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -56,7 +56,8 @@ pyo3-log = { version = "0.9.0"}
 pyproject-toml = { version = "0.8.0" }
 rand = { version = "0.8.5" }
 rayon = { version = "1.8.0" }
-reflink-copy = { version = "0.1.11" }
+# For correct IO error handling: https://github.com/cargo-bins/reflink-copy/pull/51
+reflink-copy = { git = "https://github.com/konstin/reflink-copy", rev = "1fc25b9ca5087bd20f78546009fe98709e9c4343" }
 regex = { version = "1.10.2" }
 reqwest = { version = "0.11.22", default-features = false, features = ["json", "gzip", "brotli", "stream", "rustls-tls"] }
 reqwest-middleware = { version = "0.2.4" }
diff --git a/crates/install-wheel-rs/src/linker.rs b/crates/install-wheel-rs/src/linker.rs
index 24c775f13..ad3ec0c60 100644
--- a/crates/install-wheel-rs/src/linker.rs
+++ b/crates/install-wheel-rs/src/linker.rs
@@ -297,7 +297,8 @@ fn clone_wheel_files(
 
     // On macOS, directly can be recursively copied with a single `clonefile` call.
     // So we only need to iterate over the top-level of the directory, and copy each file or
-    // subdirectory.
+    // subdirectory unless the subdirectory exists already in which case we'll need to recursively
+    // merge its contents with the existing direcotry.
     for entry in fs::read_dir(wheel.as_ref())? {
         let entry = entry?;
         let from = entry.path();
@@ -305,20 +306,42 @@ fn clone_wheel_files(
             .as_ref()
             .join(from.strip_prefix(&wheel).unwrap());
 
-        // Delete the destination if it already exists.
-        fs::remove_dir_all(&to)
-            .or_else(|_| fs::remove_file(&to))
-            .ok();
-
-        // Copy the file.
-        reflink_copy::reflink(&from, &to).map_err(|err| Error::Reflink { from, to, err })?;
-
+        clone_recursive(&from, &to)?;
         count += 1;
     }
 
     Ok(count)
 }
 
+fn clone_recursive(from: &Path, to: &Path) -> Result<(), Error> {
+    // Attempt to copy the file or directory
+    debug!("Cloning {} to {}", from.display(), to.display());
+    let reflink = reflink_copy::reflink(from, to);
+
+    // If copying fails and the directory exists already, it must be merged recursively
+    if from.is_dir()
+        && reflink
+            .as_ref()
+            .is_err_and(|err| matches!(err.kind(), std::io::ErrorKind::AlreadyExists))
+    {
+        for entry in fs::read_dir(from)? {
+            let entry = entry?;
+            let child_from = entry.path();
+            let child_to = to.join(child_from.strip_prefix(from).unwrap());
+            clone_recursive(child_from.as_path(), child_to.as_path())?;
+        }
+    } else {
+        // Other errors should be tracked
+        reflink.map_err(|err| Error::Reflink {
+            from: from.to_path_buf(),
+            to: to.to_path_buf(),
+            err,
+        })?;
+    }
+
+    Ok(())
+}
+
 /// Extract a wheel by copying all of its files into site packages.
 fn copy_wheel_files(
     site_packages: impl AsRef<Path>,
diff --git a/crates/puffin-cli/tests/pip_sync.rs b/crates/puffin-cli/tests/pip_sync.rs
index ee3abbb95..6c313f523 100644
--- a/crates/puffin-cli/tests/pip_sync.rs
+++ b/crates/puffin-cli/tests/pip_sync.rs
@@ -521,6 +521,8 @@ fn install_git_subdirectories() -> Result<()> {
     });
 
     check_command(&venv, "import example_pkg", &temp_dir);
+    check_command(&venv, "import example_pkg.a", &temp_dir);
+    check_command(&venv, "import example_pkg.b", &temp_dir);
 
     Ok(())
 }