I also do not have chain gang.

It was formerly the Lumeris homeworld and I took it, if that matters at all.

I've attached the save

lost population.sav

Sorry for this thread necromancy, but there is a contextual workaround for this I just discovered. The food stock will reset to zero once the population is zero, so if you have just few enough pops that they can all fit in the spaceport, just move them to the spaceport and then back into the system and you should get the correct growth for your actual food production. This bug, like the old one that would mess up the empire summary screen, (actually, that one might still exist...the conditions just haven't come up for me in game in a while) probably has to do with (1) wiping out whole populations during an invasion and (2) capturing systems that have been turned into hunting grounds/pirate territory/&c. In both cases, what seems to be going on is that there are "less than one" pops of one or more species there, which I believe is an intended feature designed to help species on a conquered or assimilated planet recover their numbers, but it sometimes interacts in an unexpected way with the game's other mechanics.