Perhaps this is causing it in data-updates.lua, should conditionally call code, should never conditionally require files. All files must be required in the same order at the same time in all cases regardless of settings or anything:
if settings.startup["necro-setting-support-ne_enemies"].value == true then
require("prototypes.updates.updates-corpses_nee")
end
In short, the server won't be able to sync mod settings to the client if they differ if files are conditionally loaded as the hash comparison will fail. It can be worked around be leaving the settings default (they weren't in this case), or copying the mod-settings to the client.
