If you happen to be on Windows then chances are known file extensions are hidden and if you rename a file in the explorer, say
file.txt, Windows lets you rename only the first part so it becomes
file.plantuml.txt. You can google
windows show known file extensions or something to find out how to change this.
You could now either keep manually setting the syntax to PlantUML like you did, or try renaming the files in Atom by right-clicking a file in the tree-view and selecting rename. That should let you change the extension as well.