diff --git a/app/services/submission/plant_line_parser.rb b/app/services/submission/plant_line_parser.rb
index 766c9809b..3012511b0 100644
--- a/app/services/submission/plant_line_parser.rb
+++ b/app/services/submission/plant_line_parser.rb
@@ -18,16 +18,7 @@ def call
       @upload.log "Detected wrong file format - please make sure the file is not encoded (e.g. you are uploading an xls, instead of a text file)."
     end
 
-    if @upload.errors.empty?
-      @upload.submission.content.append(:step03,
-                                        plant_line_list: @plant_line_names,
-                                        new_plant_lines: @new_plant_lines,
-                                        new_plant_varieties: @new_plant_varieties,
-                                        new_plant_accessions: @new_plant_accessions)
-      @upload.submission.content.update(:step03, uploaded_plant_lines: @plant_line_names)
-      @upload.submission.save!
-      @upload.submission.content.save!
-    end
+    update_submission_content if @upload.errors.empty?
   end
 
   private
@@ -79,6 +70,36 @@ def parse_plant_lines
     @upload.log "Detected #{@new_plant_varieties.size} plant line(s) of new (i.e. not existing in BIP) plant variety(ies)."
   end
 
+  def update_submission_content
+    remove_overriden_content
+    append_uploaded_content
+
+    @upload.submission.save!
+  end
+
+  def remove_overriden_content
+    current_new_plant_lines = @upload.submission.content.new_plant_lines || []
+    current_new_plant_varieties = @upload.submission.content.new_plant_varieties || {}
+    current_new_plant_accessions = @upload.submission.content.new_plant_accessions || {}
+
+    overriden_new_plant_lines =
+      current_new_plant_lines.select { |npl| @plant_line_names.include?(npl.fetch("plant_line_name")) }
+
+    @upload.submission.content.update(:step03,
+                                      new_plant_lines: current_new_plant_lines - overriden_new_plant_lines,
+                                      new_plant_varieties: current_new_plant_varieties.except(*@plant_line_names),
+                                      new_plant_accessions: current_new_plant_accessions.except(*@plant_line_names))
+  end
+
+  def append_uploaded_content
+    @upload.submission.content.append(:step03,
+                                      plant_line_list: @plant_line_names,
+                                      new_plant_lines: @new_plant_lines,
+                                      new_plant_varieties: @new_plant_varieties,
+                                      new_plant_accessions: @new_plant_accessions)
+    @upload.submission.content.update(:step03, uploaded_plant_lines: @plant_line_names)
+  end
+
   def csv
     @csv ||= CSV.new(input)
   end
@@ -97,8 +118,6 @@ def correct_input?(row)
 
     if reused_plant_line?(plant_line_name)
       @upload.log "Ignored row for #{plant_line_name} since a plant line with that name is already defined in the uploaded file."
-    elsif current_new_plant_lines.include?(plant_line_name)
-      @upload.log "Ignored row for #{plant_line_name} since a plant line with that name is already defined. Please clear the 'Plant line list' field before re-uploading a CSV file."
     elsif existing_plant_line?(plant_line_name) && !existing_plant_line_match?(pl_attrs, pv_attrs)
       @upload.log "Ignored row for #{plant_line_name} since a plant line with that name is already present in BIP "\
                   "but uploaded data does not match existing record."
@@ -192,10 +211,6 @@ def current_plant_lines
     @current_plant_lines ||= @upload.submission.content.plant_line_list || []
   end
 
-  def current_new_plant_lines
-    @current_new_plant_lines ||= (@upload.submission.content.new_plant_lines || []).map { |pl| pl["plant_line_name"] }
-  end
-
   def header_columns
     [
       "Species",
diff --git a/spec/services/submission/plant_line_parser_spec.rb b/spec/services/submission/plant_line_parser_spec.rb
index fc845a961..2627da467 100644
--- a/spec/services/submission/plant_line_parser_spec.rb
+++ b/spec/services/submission/plant_line_parser_spec.rb
@@ -140,52 +140,59 @@
     end
 
     context "override of previously defined content" do
+      before { allow(subject).to receive(:parse_header) }
+
       it 'allows override of existing plant line with existing plant line' do
         pl = create(:plant_line)
 
-        submission.content.update(:step03, plant_line_list: pl.plant_line_name)
+        submission.content.update(:step03, plant_line_list: [pl.plant_line_name])
         submission.save!
 
         input_is "#{pl.taxonomy_term.name},,,#{pl.plant_line_name}"
-        subject.send(:parse_plant_lines)
-        expect(subject.plant_line_names).to eq [pl.plant_line_name]
-        expect(subject.new_plant_lines).to eq []
+        subject.call
+        expect(submission.reload.content.plant_line_list).to eq [pl.plant_line_name]
+        expect(submission.content.new_plant_varieties).to be_blank
+        expect(submission.content.new_plant_accessions).to be_blank
       end
 
-      it 'blocks override of new plant line with new plant line' do
-        submission.content.update(:step03, plant_line_list: ["new-pl"],
-                                           new_plant_lines: [{ plant_line_name: "new-pl",
-                                                               plant_variety_name: "new-pv",
-                                                               taxonomy_term: "Brassica napus" }])
+      it 'allows override of new plant line with new plant line' do
+        submission.content.update(:step03,
+          plant_line_list: ["new-pl"],
+          new_plant_lines: [{ plant_line_name: "new-pl", plant_variety_name: "new-pv", taxonomy_term: "Brassica napus" }],
+          new_plant_varieties: { "new-pl" => { "plant_variety_name" => "new-pv" } },
+          new_plant_accessions: { "new-pl" => { "plant_accession" => "new-pa" } }
+        )
         submission.save!
 
-        input_is "Brassica napus,,,new-pl"
-        subject.send(:parse_plant_lines)
+        input_is "Brassica napus,new-pv-2,,new-pl"
+        subject.call
+        expect(upload.errors).to be_blank
         expect(submission.reload.content.plant_line_list).to eq ["new-pl"]
         expect(submission.content.new_plant_lines).
-          to eq [{ "plant_line_name" => "new-pl", "plant_variety_name" => "new-pv", "taxonomy_term" => "Brassica napus" }]
+          to eq [{ "plant_line_name" => "new-pl", "plant_variety_name" => "new-pv-2", "taxonomy_term" => "Brassica napus" }]
 
-        expect(upload.logs).
-          to include "Ignored row for new-pl since a plant line with that name is already defined. "\
-                     "Please clear the 'Plant line list' field before re-uploading a CSV file."
+        expect(submission.content.new_plant_varieties).to eq("new-pl" => { "plant_variety_name" => "new-pv-2" })
+        expect(submission.content.new_plant_accessions).to be_blank
       end
 
-      it 'blocks override of new plant line by existing plant line' do
+      it 'allows override of new plant line by existing plant line' do
         pl = create(:plant_line)
 
-        submission.content.update(:step03, plant_line_list: [pl.plant_line_name],
-                                           new_plant_lines: [{ plant_line_name: pl.plant_line_name,
-                                                               taxonomy_term: "Brassica napus" }])
+        submission.content.update(:step03,
+          plant_line_list: [pl.plant_line_name],
+          new_plant_lines: [{ plant_line_name: pl.plant_line_name, plant_variety_name: "new-pv", taxonomy_term: "Brassica napus" }],
+          new_plant_varieties: { pl.plant_line_name => { "plant_variety_name" => "new-pv" } },
+          new_plant_accessions: { pl.plant_line_name => { "plant_accession" => "new-pa" } }
+        )
         submission.save!
 
         input_is "#{pl.taxonomy_term.name},,,#{pl.plant_line_name}"
-        subject.send(:parse_plant_lines)
+        subject.call
+        expect(upload.errors).to be_blank
         expect(submission.reload.content.plant_line_list).to eq [pl.plant_line_name]
-        expect(submission.content.new_plant_lines).to eq [{ "plant_line_name" => pl.plant_line_name,
-                                                            "taxonomy_term" => "Brassica napus" }]
-        expect(upload.logs).
-          to include "Ignored row for #{pl.plant_line_name} since a plant line with that name is already defined. "\
-                     "Please clear the 'Plant line list' field before re-uploading a CSV file."
+        expect(submission.content.new_plant_lines).to be_blank
+        expect(submission.content.new_plant_varieties).to be_blank
+        expect(submission.content.new_plant_accessions).to be_blank
       end
     end