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modlist.txt follows the archives you add and remove. It was written once and then left alone, so an archive added later deployed but was missing from the load order list. Deploy now rewrites it whenever it should say something else; your next deploy fixes an out-of-date one (it shows as one change waiting).
Add mod takes a single mod file, such as an .archive, .reds or .lua, not only a zip, 7z or rar. REDdeck puts it where its type goes, and asks when it cannot tell. The command line's add does the same.