diff --git a/pom.xml b/pom.xml
index c198bf0b..640b9bdd 100644
--- a/pom.xml
+++ b/pom.xml
@@ -74,7 +74,7 @@
         <dependency>
             <groupId>org.eclipse.jgit</groupId>
             <artifactId>org.eclipse.jgit</artifactId>
-            <version>6.3.0.202209071007-r</version>
+            <version>6.9.0.202403050737-r</version>
         </dependency>
         <dependency>
             <groupId>org.jetbrains.kotlin</groupId>
diff --git a/src/main/kotlin/se/kth/spork/util/LineBasedMerge.kt b/src/main/kotlin/se/kth/spork/util/LineBasedMerge.kt
index c10b34b6..d0c1e5a4 100644
--- a/src/main/kotlin/se/kth/spork/util/LineBasedMerge.kt
+++ b/src/main/kotlin/se/kth/spork/util/LineBasedMerge.kt
@@ -63,6 +63,10 @@ fun lineBasedMerge(base: String, left: String, right: String): Pair<String, Int>
                 inConflict = true
             }
             lines.add(SporkPrettyPrinter.MID_CONFLICT)
+        } else if (chunk.conflictState
+            == MergeChunk.ConflictState.BASE_CONFLICTING_RANGE
+        ) {
+            continue
         }
         for (i in chunk.begin until chunk.end) {
             lines.add(seq.getString(i))
diff --git a/src/test/java/se/kth/spork/LineBasedMergeTest.java b/src/test/java/se/kth/spork/LineBasedMergeTest.java
new file mode 100644
index 00000000..b0b3999d
--- /dev/null
+++ b/src/test/java/se/kth/spork/LineBasedMergeTest.java
@@ -0,0 +1,27 @@
+package se.kth.spork;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import kotlin.Pair;
+import org.junit.jupiter.api.Test;
+import se.kth.spork.util.LineBasedMergeKt;
+
+public class LineBasedMergeTest {
+
+    @Test
+    public void testMergeWithDeletionsMinimal() {
+        Pair<String, Integer> result =
+                LineBasedMergeKt.lineBasedMerge("a\nB\nC\nD\ne", "a\nB\nC\ne", "a\nB\nD\ne");
+
+        assertEquals(
+                "a\n"
+                        + "B\n"
+                        + "<<<<<<< LEFT\n"
+                        + "C\n"
+                        + "=======\n"
+                        + "D\n"
+                        + ">>>>>>> RIGHT\n"
+                        + "e",
+                result.component1());
+    }
+}