Yes, you may file your 2016 return without withdrawing the excess HSA contribution for 2016.
To avoid the 6% penalty, though, you would need to amend your 2016 return, since that is the year to which the penalty applies.
If you file your 2016 tax return without indicating that you withdrew the excess HSA contribution, then you will be able to withdraw it in future years, but you must pay a 6% penalty on the excess contribution plus earnings, in addition to income and payroll taxes on that amount.
More information about HSA contributions and distributions
can be found in
IRS Publication 969, Health Savings Accounts.
