Yes, the contributions will stay in your HSA account until you use them. Even though you are not enrolled in High Deductible Health Plan, you can still receive tax free distributions in future years from your HSA as long as you have basis in your account.
In the year your balance goes to zero, you will not pay the 20% penalty if the distribution was for medical expenses and you will not be charged the 6% penalty because there is no excess contribution to penalize.
As far as making the decision now to take a non-qualified withdrawal now, you need to attempt to weigh the costs rather to leave the distributions in and pay 6% excise tax but receive a tax-free distribution later OR take a non-qualified taxable distribution now but not worry about future 6% excess contribution penalty each year. This is something you need to determine on your own.
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