My Belethor was killed in a vampire attack, and Ysolda is now in the shop and has the merchant option (though her dialogue still says she's going to save up from trading with the khajiit and buy the bannered mare). The problem is that the shop is never open now that Belethor's dead and Ysolda's in charge and if I go in, she and Sigurd threaten to have me arrested.
To test, I spawned a new Belethor, who immediately went into the shop and the front door became unlocked. He now stands behind the counter as he used to, and I can access the shop via Ysolda, (who seems to be standing akwardly in the wrong spot, facing the wrong direction). So the fix to transfer the merchanteering from Belethor to Ysolda, which I understand to be one of the fixes included in this patch, is working perfectly, but Ysolda didn't seem to inherhit the ability to open the store to actually conduct business.