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. That tag sits on every pressing and pulling pattern — bench and push-ups, overhead press, rows, pull-ups and pulldowns alike — so a shoulder flag takes out all of your upper-body push and pull work. Not some of it. All of it.
Any training day left empty by that 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 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.