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My muscle and stamina levels aren't conserved between saves. I accidentally went through a sex scene and then lost all my stamina and muscle levels. This occured at school as Emily was experiencing her second growth spur

Loot from the gold chests at lower levels became too op. You could get grow essences and skill crystals

I didn't figure out how to do that. I would assume it would be in the inventory save file but I didn't touch it.  Instead I made some random character and gave them 60 level up lollipops and put it all on happiness generation. For the badge coins, I gave that same resident 40 levels into storage and got a savor it badge and made the character a sweet tooth and spammed cheap sweet items

In the cardboard dungeon and the ruins temple, there will be water fountains that allow you to transmute a single essence for free per fountain

Not really. One of the options in the options menu is "open save data path" From there, you can edit the .es3 files with notepad or any text editing software. Before you edit, you should make a copy of the current save just in case something bad happens. The code should be somewhat easy to read. I'd recommend not touching levels as that causes the save to be glitchy.

Where can you access the cheats

for combat, press the squiggly button that is to the right of 1 on the keyboard to bring up the console and type "RestartLevel" and it may override the softlock

Dungeon saving threshold for the ruins past the ravine is every 20th floor. The cave in the gorge is every 15th floor