diff --git a/core/pkg/fixhandler/fixhandler.go b/core/pkg/fixhandler/fixhandler.go
index ec00a975..4a38df56 100644
--- a/core/pkg/fixhandler/fixhandler.go
+++ b/core/pkg/fixhandler/fixhandler.go
@@ -217,13 +217,6 @@ func (h *FixHandler) getFilePathAndIndex(filePathWithIndex string) (filePath str
 
 func (h *FixHandler) applyFixToFile(filePath, yamlExpression string) (cmdError error) {
 
-	// While obtaining fixedYamlNode, comments and empty lines at the top are ignored. In order to deal with that,
-	// comments and empty lines are removed and they are inserted again when applying fixes to file.
-	contentAtHead, err := truncateContentAtHead(filePath)
-
-	if err != nil {
-		logger.L().Fatal("Error truncating comments and empty lines at head")
-	}
 	originalYamlNode := constructDecodedYaml(filePath)
 	fixedYamlNode := constructFixedYamlNode(filePath, yamlExpression)
 
@@ -232,7 +225,7 @@ func (h *FixHandler) applyFixToFile(filePath, yamlExpression string) (cmdError e
 
 	contentToAdd, linesToRemove := getFixInfo(originalList, fixedList)
 
-	err = applyFixesToFile(filePath, contentToAdd, linesToRemove, contentAtHead)
+	err := applyFixesToFile(filePath, contentToAdd, linesToRemove)
 	return err
 }
 
diff --git a/core/pkg/fixhandler/fixhandler_test.go b/core/pkg/fixhandler/fixhandler_test.go
index b8b08028..06cbaab0 100644
--- a/core/pkg/fixhandler/fixhandler_test.go
+++ b/core/pkg/fixhandler/fixhandler_test.go
@@ -79,7 +79,7 @@ func testDirectoryApplyFixHelper(t *testing.T, yamlExpressions *[]string, direct
 
 		errorMessage := fmt.Sprintf("Content of fixed %s doesn't match content of %s in %s", originalFile, fixedFile, directoryPath)
 
-		assert.Equal(t, string(tempFileContent), string(fixedFileContent), errorMessage)
+		assert.Equal(t, string(fixedFileContent), string(tempFileContent), errorMessage)
 
 	}
 }
diff --git a/core/pkg/fixhandler/yamlhandler.go b/core/pkg/fixhandler/yamlhandler.go
index d52f4ea6..a129a3f8 100644
--- a/core/pkg/fixhandler/yamlhandler.go
+++ b/core/pkg/fixhandler/yamlhandler.go
@@ -88,6 +88,12 @@ func matchNodes(nodeOne, nodeTwo *yaml.Node) int {
 }
 
 func getFixInfo(originalList, fixedList *[]NodeInfo) (*[]ContentToAdd, *[]LinesToRemove) {
+
+	// While obtaining fixedYamlNode, comments and empty lines at the top are ignored.
+	// This causes a difference in Line numbers across the tree structure. In order to
+	// counter this, line numbers are adjusted in fixed list.
+	adjustFixedListLines(originalList, fixedList)
+
 	contentToAdd := make([]ContentToAdd, 0)
 	linesToRemove := make([]LinesToRemove, 0)
 
@@ -209,13 +215,14 @@ func updateLinesToReplace(fixInfoMetadata *FixInfoMetadata) (int, int) {
 	return updatedOriginalTracker, updatedFixedTracker
 }
 
-func applyFixesToFile(filePath string, contentToAdd *[]ContentToAdd, linesToRemove *[]LinesToRemove, contentAtHead string) error {
+func applyFixesToFile(filePath string, contentToAdd *[]ContentToAdd, linesToRemove *[]LinesToRemove) error {
+	// Read contents of the file line by line and store in a list
 	linesSlice, err := getLinesSlice(filePath)
 
 	if err != nil {
 		return err
 	}
-
+	// Clear the current content of file
 	if err := os.Truncate(filePath, 0); err != nil {
 		return err
 	}
@@ -237,9 +244,6 @@ func applyFixesToFile(filePath string, contentToAdd *[]ContentToAdd, linesToRemo
 	writer := bufio.NewWriter(file)
 	lineIdx, lineToAddIdx := 1, 0
 
-	// Insert the comments and lines at the head removed initially.
-	writer.WriteString(contentAtHead)
-
 	// Ideally, new node is inserted at line before the next node in DFS order. But, when the previous line contains a
 	// comment or empty line, we need to insert new nodes before them.
 	adjustContentLines(contentToAdd, &linesSlice)
diff --git a/core/pkg/fixhandler/yamlhelper.go b/core/pkg/fixhandler/yamlhelper.go
index 502c48a1..85e674fb 100644
--- a/core/pkg/fixhandler/yamlhelper.go
+++ b/core/pkg/fixhandler/yamlhelper.go
@@ -45,6 +45,24 @@ func adjustContentLines(contentToAdd *[]ContentToAdd, linesSlice *[]string) {
 	}
 }
 
+func adjustFixedListLines(originalList, fixedList *[]NodeInfo) {
+	differenceAtTop := (*originalList)[0].node.Line - (*fixedList)[0].node.Line
+
+	if differenceAtTop <= 0 {
+		return
+	}
+
+	for _, node := range *fixedList {
+		// Line numbers should not be changed for new nodes.
+		if node.node.Line != 0 {
+			node.node.Line += differenceAtTop
+		}
+	}
+
+	return
+
+}
+
 func constructDFSOrderHelper(node *yaml.Node, parent *yaml.Node, dfsOrder *[]NodeInfo, index int) {
 	dfsNode := NodeInfo{
 		node:   node,