Can you spend one production unit to offset population loss from plague cubes on a population 0 location?
For Pandemic Legacy, always follow the rules in exact order, use the rule book as a check list. You can not progress through to subsequent steps until you have completed the entirety of your current step.

During end game, if the population decreases to 0 during step 1, then that city is forsaken. It remains at population 0 until you (may) spend 2 production points during step 4.

If you want to prevent a drop in population, then build a supply centre on that location during the game, as end game Step 1 is holistic in regards to supply centres and plague cubes.

When in doubt over any of the rules, do what is in the least interest of the players.