In the mod all gui elements in screen are destroyed, which breaks other mods with things in screen. One should only destroy gui elements you know are yours.

But one example: https://i.imgur.com/eP5hvXn.jpeg

I have some tweaks which should fix it on your side, but it won't help any mods that don't rebuild their GUI every on_configuration_changed:

1) changed destroy_gui to destroy_main_gui on many lines
2) changed the name on line 32 to name="TTS_main"..index,

3)Changed the last function to:
function destroy_main_gui(screen)
  for num,elm in pairs(screen.children) do
    if string.find(elm.name, "TTS_main") then
      elm.destroy()
    end
  end
end

Forgot to add: if someone has a sleep gui open, this fix won't delete that sleep gui. I'm in the Factorio #mod-making room a lot, as well are other people who can offer advice.

This fixes seems to help out but when somebody uses this Mod + Milestones ones read through this thread please: https://mods.factorio.com/mod/Milestones/discussion/62fd06d6663e048f964062bd

THere are two commands in the mod which helped me out.

I have some tweaks which should fix it on your side, but it won't help any mods that don't rebuild their GUI every on_configuration_changed:

1) changed destroy_gui to destroy_main_gui on many lines
2) changed the name on line 32 to name="TTS_main"..index,

3)Changed the last function to:
function destroy_main_gui(screen)
  for num,elm in pairs(screen.children) do
    if string.find(elm.name, "TTS_main") then
      elm.destroy()
    end
  end
end

Thanks for the support, I'm pretty new at modding and I didn't realize that this could be a problem until I ran into it. Anyway I fixed destroying only elements of this mod, as you suggested.