Your father has far too many funds for someone with that amount of savings, and the expense ratios are atrocious. And now his "advisor" has decided that those expenses are insufficient and so your dad should move into annuities, so he (the advisor) can get, what, 7.5% up front? This is legalized highway robbery.
(Aside: I bet anything the advisor has selected so many funds as a way to persuade your dad that he *needs* the advisor to do it for him, because, wow, this investing thing is just *so* complicated, and you need this complex asset allocation and someone who is always watching the market so he can adjust that in response to market shifts to keep your dad safe, yadda yadda yadda. This is such fear-mongering bullshit that it makes me want to fly through the computer screen and throttle him.)
By way of contrast -- a/k/a out in the real world -- your dad would do just fine with a portfolio of two index funds (stocks/bonds) and cash equivalents (CDs/money markets). If that is too much, he could choose one of many target retirement date/lifecycle funds. Added bonus: your dad has sufficient money that if he were in Vanguard, he'd qualify for Admiral shares (lower expense ratios). And he wouldn't even need to go it alone -- I believe the major brokerages like Vanguard are beginning to offer some planning assistance (free) to folks above a certain investment threshold, as are other companies (I get solicitations from T. Rowe Price all the time, and I don't even have that much invested with them). I get that your dad likes the comfort of not going it alone, but wanting someone to hold his hand doesn't mean he is stuck with this rip-off.
Your first and only immediate goal is to get your father divorced from this advisor. I can't tell you whether an annuity would have a reasonable role to play in the portfolio of a conservative investor like your father. But I sure as hell wouldn't trust an answer from someone who has already demonstrated that lining his own pockets is more important than looking out for your dad's best interest. Can you set your father up with a fee-only planner to talk through his finances and goals and set up a better plan to cover his needs -- even if you need to pay for the visit yourself? Who knows, maybe an annuity is a reasonable choice for your dad -- maybe it's worth it to him to give up the gains and pay the higher fees to ensure stress-free income. But I would want to hear that from someone who doesn't have such a vested interest in the outcome.
Re: the $60K for flipping, your dad is over 60, he can take whatever he wants from his tIRA. Just remember that those distributions count as income in the year he takes them, so (a) he will need to take out more than $60k to end up with $60k in his pocket, and (b) he will want to pay attention to tax brackets when planning those withdrawals -- i.e., he may want to split his withdrawals over a few years to keep their total income within a lower tax bracket. Again, this is something that a decent advisor should be able to help him structure. Whether he *should* do that depends on whether he needs that $ to live off of; they seem to have good pensions and SS, etc., but without knowing their expenses, we can't really say. Again: this is the kind of thing an independent, fee-only advisor does.