I’m not quite sure what you’re expecting to see happen.
A couple of points might be causing confusion.
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The template file for a Collection should always be kept in Notenik’s own format, no matter what the preferred file format is for the Collection.
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YAML and MultiMarkdown formats are similar in most ways. So if you’re converting from MMD to YAML, you may not see any difference in the formatting of the files on disk. The YAML syntactical differences primarily arise for fields with multiple values, since YAML formats these differently.
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In most cases, Notenik will try to deduce a particular Note’s format from the actual file contents. Multiple formats can usually be combined in a collection with no ill effects.
It does appear, though, that Notenik might be reverting your preferred file format from YAML to MMD. Let me look into this and see what I can find.
And if you’re seeing other problems, please don’t wait to report those. They are likely independent issues.