What do the upgrade set look like in DEV? Back then, running step 2A turned every thing red which was affect and only clears when you use the merge function (step 2c).
If you complete the upgrade in DEV (starting the step will update the time stamp, but does not tell you whether the person actually did the work... but the gap between the time stamps of the steps give a fair indication...) and transport the upgrade via step 3 and then the roles then it should clear.
By the sounds of things, you should also use the cross syste comparison to check that the whole bang shoot is still in sync and bring all wanted development settings (SU24 is workbench requests) back to DEV if needed.
The report for cross system comparisons is: SU2X_CHECK_CONSISTENCY.
Cheers,
Julius