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For the Virgin logan route, you can't lose any virginities until you get his 3rd heart. The only way to do that is by not staying the night with Bernard at his house. You have to leave and then you'll still get the option to talk about Caleb after that. Then after you lose virginity to Logan, you can stay the night with Bernard, but if you bottom for logan you have to top for bernard in order to get special dialogue and reward during his axe throwing scene at the fair. That's because you can't gain sexual experience in the hole Logan used lol. 

For Victoria you just talk to her in her normal spot. For Desert, you have to get enough likes with Vadir in the mountain tavern until you unlock a talk topic for the dwarven city... i forget the name... Mag Dornal or w/e it is lol. When you travel to the city with him it will unlock the desert. 

Yes he remembers your past choices but there are not really any consequences. 

study at your hut then talk to Othra

Same happened to me. Did you use the cheat menu at all? It seems if you use cheats for restrain potion to do bernard quest, you miss out on learning restrain potion (strong) at your hut after you turn in More Potions to Bernard, so Othra can't give you the quest. Or something along those lines, I forget the specifics.... I had to restart my save and not cheat with potions to get it to work. 

Go to the ruins and it's a random encounter. Leave and go back to ruins until you get him.

Goto AppData (hidden) and Renpy folder, delete the LD folder there, as well as the save folder in the game folder.

This game is amazing! I've played a few free bara games on itch, mostly VNs. Did not know what to expect with this but it blew me away. There is SO much content, the artwork is incredible, the game mechanics are so much fun... just wow. The game is much bigger than I was expecting. I can't believe it's free. It's so polished it could easily be a paid game on Steam. I've dumped so many hours in this and still haven't experienced all the game has to offer. Can't wait to see where it goes in the future.  Thank you to all the devs who made this game <3