We don't know what you did in the past. You will need to review your prior tax returns. You may need to file amended returns to report the expenses and contributions even if it does not change your taxes.
Contributions made by payroll deduction are reported on your W-2 and should be automatically captured by any tax software and added to form 8889. Extra contributions you make out of pocket are reported on s separate line of form 8889. You must file the form to certify that you were enrolled in an eligible HDHP. Without that certification, the IRS may assume your contributions are ineligible and send you a bill for taxes and penalties.
You must also report your withdrawals from an HSA on form 8889, and certify they were used for qualifying medical expenses. If you don't certify the withdrawals, the IRS may assume your withdrawals are not qualified, and will send you a bill for taxes and penalties.
The overall point is, the IRS doesn't have to assume anything in your favor (like the fact your expenses are allowable). You have to put it all in writing.
