diff --git a/cmd/bd/doctor/legacy.go b/cmd/bd/doctor/legacy.go
index dafec81f..656e10ee 100644
--- a/cmd/bd/doctor/legacy.go
+++ b/cmd/bd/doctor/legacy.go
@@ -132,13 +132,14 @@ func CheckLegacyJSONLFilename(repoPath string) DoctorCheck {
 			continue
 		}
 
-		// Skip merge artifacts and backups
+		// Skip merge artifacts, backups, and system files
 		lowerName := strings.ToLower(name)
 		if strings.Contains(lowerName, "backup") ||
 			strings.Contains(lowerName, ".orig") ||
 			strings.Contains(lowerName, ".bak") ||
 			strings.Contains(lowerName, "~") ||
-			strings.HasPrefix(lowerName, "backup_") {
+			strings.HasPrefix(lowerName, "backup_") ||
+			name == "deletions.jsonl" {
 			continue
 		}
 
diff --git a/cmd/bd/doctor/legacy_test.go b/cmd/bd/doctor/legacy_test.go
index 6b6d63ab..9469bb57 100644
--- a/cmd/bd/doctor/legacy_test.go
+++ b/cmd/bd/doctor/legacy_test.go
@@ -225,6 +225,12 @@ func TestCheckLegacyJSONLFilename(t *testing.T) {
 			expectedStatus: "warning",
 			expectWarning:  true,
 		},
+		{
+			name:           "deletions.jsonl ignored as system file",
+			files:          []string{"beads.jsonl", "deletions.jsonl"},
+			expectedStatus: "ok",
+			expectWarning:  false,
+		},
 	}
 
 	for _, tt := range tests {