Do not rewrite relative links for system notes

app/models/note.rb

@@ -457,7 +457,7 @@ class Note < ApplicationRecord
   end
   def banzai_render_context(field)
-    super.merge(noteable: noteable)
+    super.merge(noteable: noteable, system_note: system?)
   end
   def retrieve_upload(_identifier, paths)

changelogs/unreleased/bug-63162-duplicate_path_in_links.yml

+---
+title: Fixed 'diff version changes' link not working
+merge_request: 29825
+author:
+type: fixed

lib/banzai/filter/relative_link_filter.rb

@@ -17,6 +17,8 @@ module Banzai
       include Gitlab::Utils::StrongMemoize
       def call
+        return doc if context[:system_note]
+
         @uri_types = {}
         clear_memoization(:linkable_files)

spec/lib/banzai/filter/relative_link_filter_spec.rb

@@ -101,6 +101,13 @@ describe Banzai::Filter::RelativeLinkFilter do
         .to eq "/#{project_path}/blob/#{ref}/doc/api/README.md"
     end
+    it 'does not modify relative URLs in system notes' do
+      path = "#{project_path}/merge_requests/1/diffs"
+      doc = filter(link(path), system_note: true)
+
+      expect(doc.at_css('a')['href']).to eq path
+    end
+
     it 'ignores absolute URLs with two leading slashes' do
       doc = filter(link('//doc/api/README.md'))
       expect(doc.at_css('a')['href']).to eq '//doc/api/README.md'