This is common with any game that has mods and has updates. Updates break mods, that's just a common thing in modding. Ask any veteran starbound player about the % chance an outdated mod will actually work. The answer? Slim to none unless it's a very simple mod.
The more complicated the mod, the vastly higher chances it has of being broken upon update. A simple sprite swap or perhaps an added weapon probably wouldn't be affected... but a mod that adds all sorts of junk most likely would.
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