Overhead pressing, dips, and behind-the-neck work are the movements people most often can't tolerate with an angry shoulder. RepRoute doesn't diagnose that — it just stops putting those movements in front of you.
Here's precisely what happens when you flag the shoulder. Every exercise in your plan is checked against the shoulder tag in the exercise catalogue, and the ones carrying it are REMOVED. Across the four pressing and pulling patterns — bench and push-ups, overhead press, rows, pull-ups and pulldowns — that's 332 of 342 movements, 97% of your upper body. Catalogue-wide it comes to 375 exercises, which makes the shoulder the widest cut any RepRoute injury flag makes.
What it is not is literally all of your pressing and pulling — this page used to claim that, and the claim was false. Exactly ten movements survive a shoulder flag: Band Pull Apart, Band-Assisted Pull-up, Barbell Row, Chin-Up, Close Grip Push-up, Dumbbell Row, Incline Push-Up, Knee Push-up, Push-up and Wall Push-up. Those are the gentlest rungs in the catalogue, which is usually the point. But if your shoulder objects to a wall push-up, the flag will not save you from one. A push-up appearing in your plan does not mean the app cleared it for you — swap it or skip it.
Any training day left empty by the strip is then rebuilt: the generator refills it with up to three exercises drawn from the patterns still available to you — squat, hinge, lunge, core. So you don't end the week with a blank day. You end it with a legs-and-core day where a push day used to be.
If you can still press pain-free at some angles and it's only overhead work that hurts, don't flag the shoulder — the flag is close to all-or-nothing across pushing and pulling. Start the session and use Swap on the individual movement instead. That's the finer tool, and it leaves the rest of your plan intact.