Yes - that's a caution with the cheats in TSM. They can help with some problems, but they can also introduce instabilities. ONLY click through a Quest stage if you are stuck, having accomplished the task without advancement. Playing through the long way also lets you build up to Platinum completion if your focus stays high - and you can also work on relationship with that NPC you want to keep around. Doing that quest with my Knight, I actually let her marry and have a child with the trainee she took on - which meant missing a few Responsibilities, because you can't spar or duel while pregnant! Still worth it!