[BUG] git merge sometimes loses changes from one branch

Hello Git developers,

I would like to report a potential issue in Git's merge behavior, where changes from one branch may be lost even when the other branch does not modify the same location.

Environment:
- git version: 2.43.0
- OS: Ubuntu 24.04 LTS

Steps to reproduce:
1. On branch A, modify a file at a certain location:

   @@ -1026,7 +1028,9 @@
   public final class AutoBuilderCompilationTest {
                "  }",
                "}"); 
        Compilation compilation =
   -        javac().withProcessors(new AutoBuilderProcessor()).compile(javaFileObject);
   +        javac()
   +            .withProcessors(new AutoBuilderProcessor())
   +            .compile(javaFileObject);
        assertThat(compilation).failed();
        assertThat(compilation)
            .hadErrorContaining(

2. On branch B, make no changes to this location.

3. Merge branch A and branch B.

Expected result:
- The merge should retain the changes made in branch A:

   @@ -1026,7 +1028,9 @@
   public final class AutoBuilderCompilationTest {
                "  }",
                "}"); 
        Compilation compilation =
   -        javac().withProcessors(new AutoBuilderProcessor()).compile(javaFileObject);
   +        javac()
   +            .withProcessors(new AutoBuilderProcessor())
   +            .compile(javaFileObject);
        assertThat(compilation).failed();
        assertThat(compilation)
            .hadErrorContaining(

Actual result:
- Git sometimes produces a merged result where the modification from branch A is lost, yielding:

   @@ -1026,7 +1028,9 @@
   public final class AutoBuilderCompilationTest {
                "  }",
                "}"); 
        Compilation compilation =
           javac().withProcessors(new AutoBuilderProcessor()).compile(javaFileObject);
        assertThat(compilation).failed();
        assertThat(compilation)
            .hadErrorContaining(

Additional information:
- This issue occurs even when the other branch (B) does not modify the same location.
- It appears to happen non-deterministically and may lead to subtle bugs in real-world merges.

Thanks, Cori

On Fri, Sep 12, 2025 at 6:41 AM Guo Tingsheng <CoriCraft16@outlook.com> wrote:

My only guess here would be having a non-unique merge-base, where one of the merge bases also introduced this change, so that it appears that A made no change relative to the consolidated merge base while also making it look like branch B undid the change relative to that consolidated merge base. But, that's a wild guess and I have no idea if that's related to what you're seeing or if there's some unrelated issue at play.

Can you create a testcase to reproduce this, either a repository that others can clone together with the commands to trigger it, or a bunch of commands to both create a simple repository and demonstrate the issue?

Hello Git developers,

I would like to report a potential issue in Git’s merge behavior, where changes from one branch may be lost even when the other branch does not modify the same location.

To make it easier to reproduce, I have open-sourced this example in a public repository:
Repository: https://github.com/CoriWork/bug-replay.git

You can clone the repository and follow the README.md to replay the bug!

---

Environment:
- Git version: 2.43.0
- OS: Ubuntu 24.04 LTS

---

Steps to reproduce:
1. On branch B, modify a file at a certain location: