Will the loss offset the gain I got this year? NO
Or do I have to pay taxes on the capital gain from the HSA account? NO
The HSA is an entirely separate, tax-protected account. Nothing that happens inside the account has any affect on any other part of your tax return.
The HSA is simply money in–money out. If you are eligible to put money in, you get a tax deduction. If you take money out, it's tax-free if you use it for qualified medical expenses and taxable if you use it for other purposes (with a penalty depending on your age.). You don't pay taxes on gains inside the account and you can't take a deduction for losses that might happen in the account.
