If you filed a return showing that you owed $5000, you owe the $5000.
If you believe the return you filed was incorrect, you fix that by filing an amended return. On the amended return you indicate that the W-2 is for difficulty of care payments. Here are some articles on how to do that.
https://ttlc.intuit.com/turbotax-support/en-us/help-article/form-w-2/qualified-medicaid-waiver-payme...
https://ttlc.intuit.com/community/taxes/discussion/difficulty-of-care-payments/00/3126610
The amended return will calculate your new tax amount. If the new tax amount is less than the amount you already paid (considering withholding and all other payments) you will be claiming a refund when you file the amended return. Here are instructions on how to file an amended return.
https://ttlc.intuit.com/turbotax-support/en-us/help-article/tax-return/amend-federal-tax-return-curr...
