Jim Baen's Universe was a separate venture from Baen Books. They were only related by persons of Eric Flint, Mike Resnick et al.
I don't think Baen Books themselves are in any trouble. They keep putting out great books every month. Actually, it seems one of the biggest gripes they have now is that S&S gives them too few monthly slots, that was probably the reason David Weber did Safehold series with Tor.
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