I don't think I see any problems. I tried to raise cooking to 30, created an imprint and started new game. I went to the cave, loaded an imprint and my farming skill changed from 1 to 30. I could learn all skills that require farming 30, my work success chance was higher and my training chance was lower. Everything woked as intended.
When you finish the game and unlock imprints, the game will save the stats of the character you finished the game with. When you start new game, you can use the imprint machine to replace your new characters stats with the stats of the old character. They don't add together, they get replaced. Imprints store both the physical atributes and skill stats, but not the skills and recipes you learn from NPCs. This means that training will be less effective depending on the stats you have gained from imprinting.