Don't know about the conversion over to certificates for IRAs & Mutual Funds, but do know that I'd want the physical asset if I thought the bottom might fall out and the sides fall down. You may want to weigh how the penalties and IRS cut would be vs. how much you feel you might lose worst case. If they're just mutual funds, there should be any penalties, only cap gain taxes, unless it's tied to your IRA or 401K and depending on your age.
I watched fellow employees who do not watch, monitor or actively manage their 401Ks, take a beating, a serious beating by allowing their accounts to ride that roller coaster down, sustaining 50-60% losses, some twice in the last 20years. I caught mine and held it at around 25-30% loss and managed to build it back within the year. Point being, IMO, brokers make money when you contribute, when you win, when you lose and when you do nothing, so you may want to consider if a withdrawal loss might be less than what you think you could lose in the coming months or years.
Don't know how much you're considering to deal with, but in the early 80s I had some experiences w/ folks that dealt in gold & silver bullion & coins. I'm a big fan of silver and have been since then. I personally feel that silver is either too low or gold is too high. For hundreds of years (if not longer) the spread between the two was around 20:1. In the last half century, it has moved to around 50:1 spread on average. I translate that as silver being under priced or gold overpriced. (I'm no broker or commodities agent, I just play one on TV).
That said, something I always recommend to preppers or anyone that wants the physical item, is to consider what's called 'junk' 90% silver U.S. coins. A 'bag' is $1,000. face value, breaking down to approx. 715 troy oz. That's roughly $13,241.80 cost at Friday's close of $18.52/oz plus whatever the dealer markup/commission is. Buying any precious metals, coins, ingots, etc. carry a surcharge/commission that is the dealers cut, based upon the denominational or weight size of the product you buy. In other words, a 100oz bar costs less per oz commission than ten 10oz bars of the same metal. Same rule for the demonimational items. Commision for a 1oz coin is less per oz than a number of 1/2 or 1/10 oz coins.
I like the circulated 'junk' U.S. because it is recognized through the U.S. and doesn't require the scrutiny that 10,000 difference bar producers might generate, plus a mixed bad is multi-denominational with dimes, quarters and halves, which makes for easier use if needed.
Of note, but I don't know how it will factor in, China just granted approval for their citizens/subjects to own silver and silver is more widely used today in industry than ever before.
I'll send you a bill once you make your exchange or you can just send me a few coins.
Just for reference, have had no dealings w/ these people -
http://www.apmex.com/Category/17/90_Silver_Coins_Rolls__Bags.aspx