Skiplagging (taking only part of a one-way itinerary with no checked bags) is pretty well known at this point, and most flyers do it to either hop off at the connecting airport on their itinerary, or fly a different airline to a different destination (which I've done in the past). However, my question is:

What extra risk is there to skiplagging with an airline, and flying an onward ticket _on that same airline_? Say I'm connecting on Frontier in Denver, on like an LAX to DEN to ATL itinerary. I hop off in Denver and switch to a DEN to DTW flight that I booked separately. If I need to use the check-in counter in Denver, would the agent see my DEN to ATL reservation, or not because I already got the tickets for it?

Any insight from anyone comfortable talking about this would be much appreciated. If skiplagging posts aren't appropriate for this forum, feel free to discard this as well...