EDIT: Thanks for all the answers! Turns out I'm an idiot and chased after the wrong guy. I'll leave this post here so others can find help in this matter.
ORIGINAL POST: I came across a major bug last night when I started doing the bounty hunt quests available through building the Warden's Lodge. My second mission was to kill Sly Cyrdel at Margran's Fork. When I found and beat him and his posse he was begging for his life and I had the option to throw him in prison instead of outright killing him. Interested to see what would happen if I chose this option, I imprisoned him, thinking that I could always kill him later if required. I then went on questing for a few more (rl) hours.
When I tried to turn my bounties in, the Sly Cyrdel quest still showed up as not completed, so I went to my prison. There I was offered the option to whip the guy or release him - not to execute him. First I tried releasing him, but that just made him disappear (seemingly forever), then I manually opened his cell door, but wasn't allowed to attack him. Whipping him also had no effect.
Baffled, I googled the problem and noticed that it first came up back in 2015 with a simple note saying something along the lines of "oh yeah, if you imprison him, that's it - nothing you can do AND YOU WON'T RECEIVE ANY ADDITIONAL BOUNTY QUESTS EITHER!".
Well, that was 1.5 years ago so I figured there must have been a solution by now. I tried to reach Obsidian's customer support, which for Pillars directed me to this forum or Paradox' customer support... which doesn't even list Pillars in their help section...
So, I'm asking my question here: If imprisoning Sly is an option, there really should be a solution for this by now - I'm sure I'm not the only one having this problem. It's not really a new either, is there really no other solution than to forfeit hours of playtime and load some old save game?