I recently had our fee-only advisor ask the same question of Schwab, the custodian of our funds. Their answer was that they can only rehypothicate assets in client margin accounts that have a margin balance, and then only up to the limit of the margined position. FINRA who regulates brokers (unlike CFTC who regulated MF Global) requires Schwab to allocate 102% of the rehypothicated balance as cash to the client account from whose assets were hypothicated. Schwab currently sports about a 13.4 leverage ratio so they aren't too overleveraged. 

The question I have asked is whether Schwab can transfer our account to an affiliate in  a jurisdiction with more lax regulations - as MF Global apparently did when they transferred client accounts to a British affiliate. To me, that is as big a danger as whether or not they can rehypothicate assets.

WHY would you want your funds to be over SPIC insurance limit is perhaps the first question I would review.  Further on the cash-- as I understand it-- cash is covered  by FDIC insurance only up to 250K ?  but that is something to verify. 

You aren't even covered by basic insurance because your accts. are over the limit sounds like. So- even if MSSB fails due to other reasons- you aren't covered.Personally I would rebalance pronto to get that in order.

I would get in touch with the legal dept. directly if it were my $. I would also think of using a few houses & diversifying my funds. A lot of work, some expense -- but then I lost $$$ at MF-- so I think well worth the extra pre-caution.

after have worked for many BD's, I have found for the most part the brokers really don't know if they funds are or are not segregated.  I never knew if what my manager was tell me was correct.  Mainly because he didn't work in legal.  If the broker will put in writing and on their letter head and the branch manager and broker sign it, then maybe you will be ok.  Otherwise, it's you call.

ask the broker if he will guarantee the segregated funds personally. in writing.