what I have done is denial letter is in the reference letter supporting doc since it is with the letterhead and i have mentioned in the LOE page wise what all documents I have provided in that sectionYou should include your HR's denial in the LoE explaining why have you used a notarized letter instead of ..
Simply put a 'Refer to Appendix 1.x on your LoE' and attach the HR's letter appropriately.
All other supporting docs like your promotion/appraisal/depuatation letters, pay stubs go with your notarized reference letter.
Btw you could have used an official mail from your colleague's official mail id saved as pdf instead of notarization. But notarized ones work fine as per many other posts.