How to allocate downtime while in a Setup?
Setups do not always go to plan — here is how to record a stoppage that happens partway through a changeover and get back to the setup afterwards.
Step 1 — Press Downtime
While the line is in Setup, press the Downtime button below the speedometer.

Step 2 — Allocate the reason
Select the category, select the reason, then press Set Reason.

The reasons offered here are only those set up for the Setup state. If the reason you are looking for is missing, that is why — it will need its group updated in Fusion Manager before it appears during a setup.
Pressing Downtime does not change the state on its own. The setup keeps accruing until you press Set Reason, so commit the reason rather than leaving the panel open.
Step 3 — Resume the setup
Once the problem is cleared, press Setup to carry on. The line moves into running on its own once counts are detected and the threshold is reached.

If counts are not coming through at all — a disconnected line, or a stopped counter — pressing Setup will not hold. The line keeps whatever state was last committed until counts start arriving again.
How it appears afterwards
A stoppage inside a setup is its own state, recorded as Downtime in Setup. On the Console it shows red, exactly like any other downtime, so the lamp alone will not tell you which you are looking at.
In Analytics it may appear orange, in its own Setup Downtime class alongside planned downtime, unplanned downtime and running slow. That is a reporting colour and it is not applied in every report, so treat it as "may appear orange" rather than a guarantee. The Events Chart and the Edit Log are where the two are reliably distinguished.