Since the update that added fluoroketone to railguns, I can no longer load ammunition into them. I’ve tried dismantling and rebuilding them multiple times, and even changing the type of inserters or loaders, but the problem persists. Maybe there’s something I’m missing... has anyone else run into this issue?

Could you give me your save? https://catbox.moe/ works if <= 200mb

sure. Check out the latest spaceship called "work in progress", the only one with railguns

https://files.catbox.moe/lpoac6.zip

Oh wow, epic save.
During testing I only checked if it loaded from one spot—loaders work from any spot and (apparently >.<) inserters from many spots target the invisible assembler which handles fluoroketone.
You can identify if the inserter is targeting the invisible assembler by the insertion target coming up as a 1x1 box within the railgun, if the entire railgun is highlighted ammo will be successfully inserted.
Will get this fixed for 1.3.40, thanks for the report!

Happy to have contributed. I hope I won't have to wait long before launching the mothership toward the edge of the universe : )

Here is a pre-release version: https://files.catbox.moe/bnoc06.zip
Rename to "exotic-space-industries-remembrance_1.3.40.zip" and drop in factorio mods folder.

There are rough edges to smooth—spidertron recipes are under review and particularly some more UPS to be reclaimed from the new spidertron smart weapon cycling, but railguns can be loaded.
It'll need to be deleted manually when 1.3.40 is pushed to the mod portal.
Best of luck with the mothership!

Also, check out https://mods.factorio.com/mod/recipe-icons-improvement-for-esir if you haven't already :)

I've done everything and it seems to be working well. Thanks, and thanks for the advice as well.