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I can't buy the same funds back in Betterment. Betterment doesn't offer the market universe; it only has six Vanguard stock ETFs. So yes, I am locking in losses if I sell.
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Ok, I didn't realize what Betterment offers, so I unfairly took you to task on the "locking in" statement.
I will still take you to task on the fundamental way you're approaching this. I will restate, as others have stated, that how much you're up or down is completely irrelevant to the sale. You shouldn't even be considering that.
In your OP you say "I feel like the energy and pharm funds are just in a terrible spot right now". If that's the case why would you want to be holding these funds?
On the other hand, you later imply that you feel they will outperform. If that's the case, then why are you thinking of selling any of them?
I think you're too fixated on your paper gains/losses.
If, as you said, these investments don't fit your current strategy, then it's simple - sell them; chalk up the losses to a learning experience and move on.
If, on the other hand, you think these funds are a "good buy" at today's prices, then hold on to them, and re-evaluate in a year's time.
Finally, if you want to be rid of your advisor, then just move the funds to a regular brokerage account. That'll give you the flexibility to keep or sell the shares when you feel it's right.
Also, if you're going to go to an index-fund-based strategy you may be better off saving the 0.15% that Betterment charges and doing it yourself. I doubt that the results will be very different.
The good news here is that you're learning some lessons before you have a huge amount of money at stake.