Your comment in the first paragraph about him "transferring the earnings from company A to Company B needs to be challenged. That ain't legal! Since this is third hand: "I have a FRIEND.....", I wonder if you have the facts right?
Company A has to file the appropriate tax return (sounds like a Schedule C) which will make the profits taxable to the 100% owner (Mr. X). If he then puts the money into Company B, that would have to be an after tax transfer (loan) to Company B from Mr. X. The whole question you are asking falls apart because your premise is wrong. How do you know (or how does your friend know) he is doing what you describe? Basically, if this is true, we need to know on what basis this is being done, but you are at least two steps removed from the situation so your knowledge is going to be limited I would assume.
Yes, there are certainly controlled group issues (as Bird has noted), but I don't think this even gets that far.
If she wants to put her job at risk, then she can call the DOL and complain that she isn't being covered by a retirement plan because her boss is practicing tax fraud! Probably won't go over too well with the boss.