[Suicide Junkie]

But even if the refit would take the organics and radioactives into a minus position, the production was such that organics and radioactives storage increased by over 12,000

Unfortunately, that is not good enough.
The retrofits happen before resource income is added.
Also, if you only have 50,000 storage, you can only do $50,000 worth of retrofits each turn, even if you have a +250,000 budget surplus.