"I have not received any notification that I am over for 2021"
The only entity that will report that you have made excess HSA contributions is TurboTax while doing your tax return. The HSA custodian may imply that they know, but they don't, because they don't know what is going on your tax return.
Employers and third party entities are a constant problem in that you just never know what they are actually going to deposit an HSA contribution - even when they tell you they will do it by a certain date for a certain year, they can't be depended on to actually do it.
The safest thing for you is for you to not play too close to the edge. Contribute most money through your employer, because this saves you Social Security and Medicare tax (HSA contributions are not subject to either), but in February or March or so, check what has actually been contributed by your employer and third party benefits group, and then make a direct contribution to your HSA to fill up the year. MAKE SURE the HSA custodian understands that this contribution after the end of the year is for the previous year.
"The TurboTax software asks me to enter the amount from line 48 on my 2021 Form 5329. I do not have a Form 5329 and I want to make sure that I take care of this issue correctly. "
When you entered your 2021 return into TurboTax, you did not enter data showing an excess, because you had been misled as to when deposits had been made. So there was no 5329 to show the penalty for the carry over of excess contributions to 2022.
To fix this situation, you will have to stop working on your 2022 return, go back and amend our 2021 return to show the actual HSA contributions (which should trigger the excess), let the 2021 excess carry over to 2022 (you can no longer withdraw the 2021 excess because it needed to have been withdrawn by the due date of the 2021 return), then do your 2022 return.
To do your 2022 return, you have two choices: (1) delete what you have done so far on 2022 and re-import the 2021 return to 2022, or (2) resume what you are doing in the 2022 return and when you are asked if you overfunded your 2021 return, answer Yes and then when you asks you how much excess contributions were carried over, enter the amount of the excess that was reported to you when you amended your 2021 return.
If you continued to maximize your HSA contributions in 2022, then this carry over will likely cause another excess on your 2022 tax return.
"Do I just put the amount that I have calculated that I am over? " No, put the amount you are over when you amend your 2021 return.
"Do I subtract the amount that I am pulling out to correct the issue? " No, the withdrawal of excess contributions is not retroactive.
"Also, I have a large chunk of my HSA invested, so do I need to include the invested amount in that total? " Your 5498-SA for 2022, if you have it yet, will have a box with the value of your HSA for 12/31/2022. If you don't have the 5498-SA for 2022 yet (HSA custodians are lackadaisical about when they send this), just go on the website and see if it tells you and in the worst case, just call them and ask.
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