This is bureaucrat-think run amuk.
Conrail had class lights on all, or almost all, of their power. The older ones were true classification lights - the lights had moveable filters that worked, green for passenger, white for extras, red for helpers at the rear - and this was on power ordered LONG after Amtrak and deregulation made passenger/extra identification obsolete.
On the newest road power, these lights were give red lenses and were used to identify helpers at the rear, or light engine movements, or power standing on the main - an alternative to leaving the headlights on dim. NORAC required the head end illuminated at all times; but power standing with the headlight dimmed confused motorists at grade crossings.
CSX...I don't know at what time, but somewhere along the line they decided that the "class" lights were obsolete. New power didn't have it. Older power had them removed at rebuild, patches welded on.
But, as Conrail power was absorbed into the CSX pool, the company was MANIC to remove these "class" lights. Even before repainting, the lights would be removed and patches welded or bolted on. It somehow became a top priority; hardly any ex-Conrail power has class lights now (some of the new repaint units kept them; it seems the Power Desk lost interest and some EMD WhisperCabs kept their red marker lights).
So why remove them and tape over the holes? Possibly a job was interrupted by the ever-present shortage of operable power. And possibly the candidate engine just got lost in the (again, ever-present) pandemonium.
CSX has a problem with priorities. When rear lighted number boards went out of fashion, UP and BNSF were content to paint over the Plexiglas and paint numbers on the skin. Not CSX; they removed the bulb racks and switches; but THEN ORDERED UP STICKERS TO PUT BELOW THE NUMBERBOARDS stating that the lights were removed in accordance with the numbered company directive!
This is typical of the nuttiness rampant in Jacksonville.