You should be able to "cram down" the unsecured portion of your HELOC in Chapter 13. That means if you're upside-down on the second mortgage (e.g., your first mortgage is $200K, and your house is worth $240K, you would owe $60K more than your house is worth) you should be able to get the debt in excess of the value of the house discharged, (in the example, that $60K, and then you would only owe $40K on the HELOC).
If you're not upside-down, the debt remains secured.

