I killed the NS, and all of mafia's beecore stuff disappeared. The 'B' foods appeared in the consumables list, for example, and the bee enounter window timers disappeared (and fighting a bee didn't make a new bee window appear).
That is very strange.
There are two places in KoLmafia where we set the "king liberated" flag.
1) When you log in and we read api.php and it says "freedralph=1"
2) When you visit lair6.php (the top of the Naughty Sorceress's lair) in the Relay Browser and we see the URL "ascend.php" in the page text.
I just finished day 1 of another Beecore run, so it will be a little while before I can fetch the page text for visiting the top of the tower while there is still a prism there, but I don't understand why it would suddenly decide for you that King Ralph was free if there is the prism URL rather than the gash URL on the page.
It's never done that for me.
Visiting my char sheet, refreshing the session, logging in and out, restarting mafia didn't do anything to fix it.
So in other words, when you logged in and we fetched api.php, KoL itself said "freedralph=1". KoL itself said that you freed the king, and KoLmafia believed it.
I think you did free the king.