Pandas get_dummies() rows dropping after joining back with X
Can you post your code when you join the datasets? It's possible you're joining in a different way than you had intended. See the following helpful tutorial for figuring out exactly how you want to join datasets: https://pandas.pydata.org/docs/user_guide/merging.html
Additionally - I would check that the X and dummy dataframes have the same indexes. It's possible that in your join these forgotten entries simply don't share the same index in both dataframes.