Not dumb at all - better to know beforehand than repent afterward.
There could be tax due on the sale of the taxable account. Depends on how much the value has increased above what you contributed, how much is short term vs. long term capital gain, your total taxable income including those capital gains, etc.
Don't know about Betterment, but other brokers have a "what if?" application that tells you the tax implications if you choose to sell some or all of your holdings. Might be worth poking around the web site, or calling them. Or maybe a Betterment maven will chime in....
Can you fund the HSA out of cash flow instead of re-purposing the Betterment funds?