You will get a Form 1099-SA if you paid for medical or other expenses from your HSA or MSA during the tax year.
You should not file your tax return without entering your 1099-SA if you paid medical expenses with your Health Savings Account (distribution) during the tax year.
The IRS will be able to crosscheck this form with your tax return to make sure you entered the information. If you don't enter your 1099-SA, the IRS will make your entire distribution taxable.
Click here for a link which details information regarding your Form 1099 SA.
Also consider these helpful articles from Turbo Tax regarding HSA's:
So, considering it was filed without the 1099-SA, will the IRS simply reduce the refund amount assuming all of the missing 1099 was taxable, will the reject the entire return with a notice, or will they issue the full original refund amount and later send a notice for the bill due if no amended return is filed?
Possibly. It likely won't be caught until down so I would advise you to file an amendment to include your 1099-SA.
To avoid unnecessary delays, do not amend until your original return has been fully processed.
You can e-file your 2022 amended federal tax return.
Allow 16 weeks for processing.
See this TurboTax FAQ for help with amending.
You can check the status of your amended return here, but allow 3 weeks after filing for it to show up.
Absent a Form 8889 reporting this amount as having all been used for qualified medical expenses, the IRS is likely to treat this as unreported income subject to tax and, if you are under age 65, to a 20% additional tax, and issue a notice showing a balance due.