I think Whelan simply didn't know. Now that she knows, I think she will reinstate the patents. It's probably just a slow process.
It might not be easy to do now that the two-year window has closed, but it wouldn't cost much money, and I can't see the USPTO putting up much of a fight because the USPTO has no reason to deny reinstatement.
Whelan has to say that non-payment was "unavoidable." Here's a sample sob story, spoken with a wavering voice: "My dad was the CEO but he died and we couldn't hire a new CEO so I became the CEO because nobody else would do it and I didn't know that patents needed maintenance payments and the high school kid who works in our mailroom was throwing out letters addressed to my dad and the email address you have for us is wrong so I never saw the USPTO letters and I would have never known the patents had expired if a kind and benevolent shareholder hadn't found the problem and posted it on a stock message board." sniff.
The patents were collateral on her IBEX loans but then the Export-Import bank stepped ahead in line. The patents are collateral on that EX-IM loan now, but the EX-IM bank will probably never call in that loan, just as the SEC will probably never demand payment of the fine. The EX-IM Bank and the SEC are government entities that have no incentive to destroy a little mom-and-pop operation like BIEL as long as BIEL keeps their nose clean.
If/when they do a R/S and print new shares, though, they better do a complete and thorough job of registering the new shares. The SEC's evil eye of Sauron will be upon them, watching from above.
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