Brokerage accounts setup under Employer EIN

What's the remedy?

Is there any harm in keeping it that way?

At the brokerage house, they would have to create all new accounts with a trust id and transfer them from the old accounts.  Evidently there's lots of paperwork involved.

Consider whether not correctly recording the owner and nature of securities accounts and other investment-related accounts could result in generating tax-information reports—including, for example, Forms 1099-B, 1099-DIV, 1099-INT, which might suggest capital gains, dividends, and interest to be shown in the tax return of the organization with the Employer Identification Number.

If they aren't reporting dividends and such then there's really no harm. One of many thing that's not "right" but there are no consequences.

If the brokerage firm screwed this up, why wouldn't they be happy, more than happy, to make it right?  I'm assuming the account(s) are for a plan trust.  If they are whining about paperwork, then employer needs to find a new broker, asap.  There may be unintended consequences, or as Dick Rumsfeld would say, unknown unknowns.

Brokers will code the account - qualified plan so no tax reporting.   But issue could arise if someone takes a distribution and has withholding.  I realize employer can report under employer EIN and mark for 945 but the employer likely has a fast deposit requirement.  I've seen by the time the broker sends the withholding, it gets deposited and someone does EFAST, time goes by.   And a late deposit of withholding gets costly fast.  We apply online to get a plan EIN and use it for tax withholding reporting purposes.  

We had this happen recently.  Separate cash balance plan account and 401k plan account... but both under employer EIN.  Worse, neither account reflected the plan name (cash balance or 401k).  Applied for TIN for each plan.  Sent client's authorization letters (one for each plan) to brokerage firm with full plan names and corresponding TIN's.  Two new accounts were created, and assets moved from the old plan accounts to the respective new plan accounts.  Seemed rather painless...

Years ago, had a client in CA that did not have separate EIN/TIN and CA was very aggressive in getting client to pay taxes the state felt were due from the retirement account since it had the same EIN as employer.  It was painful to resolve so it would be worth getting the accounts correct IMO