When it comes up with the missing items, it means that Forge wants to safely remove all the blocks and entities that it lists from the world. Using /fml confirm tells it to do just that. If your map is large, it can take some time, which is why it would seem like it does nothing. I’d recommend just trying to remove Sponge first, and see if it comes up with the same issue as before, and if it does, you will need to report the issue to the GalacticCraft Developers. If it doesn’t, I’d suggest reporting it both on the GalacticCraft and the SpongeForge issue tracker, between them they should be able to find the issue, and find out which mod is causing it.