Digital learning environments record learners' responses to individual items, making it possible to study the development of specific skills rather than overall scores. Drawing conclusions about learning from these data requires a model that links responses to latent skills and tracks how mastery changes over time. When the skills measured by each item are unknown, the analyst must decide whether to estimate this structure, the Q-matrix, jointly with the learning process, or to establish it first and study learning afterwards. We show that this decision can change substantive conclusions about how learners develop. Using dynamic cognitive diagnostic models, we analyse data from two reading games measuring vocabulary and comprehension from Grade 2 to Grade 3, with item-text embeddings providing prior information for the unknown Q-matrix. A joint analysis and a bias-corrected stepwise analysis agree that most learners move toward mastering both skills, but disagree about how many remain only partially proficient at Grade 3, changing how reading progress would be reported. A simulation study identifies when the two analyses diverge and shows that joint analysis is more reliable when the item-skill structure is uncertain and the item pool changes between grades. We provide R code for both analyses.

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