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Under DOpus Magellan, AmiSync's commands in the Tools menu are now labelled "AmiSync: Status...", "AmiSync: Rescan All" and so on. Magellan has no sub menus, so it ignored the "AmiSync" sub menu and listed the commands unlabelled among other programs' tools, under a dead "AmiSync" entry. Workbench 3.9 and 3.2 still show the sub menu.
Thanks to @FerryA1.
Download amisync-0.10.6.lha below, or see the README.