Due to a bug in the underlying library for KiCad file processing text properties like visibility or styles will not be properly saved. This affects all symbols in the touched library not just the newly generated ones. Things like datasheet links or footprint assignments which are usually hidden by default will be visible now if you add a symbol to a library with Ki-nTree. Therefore I would recommend to save newly generated symbols to a buffer library for now and copy them to the target library by hand afterwards.
For more details check the bug on the kiutils page: mvnmgrx/kiutils#120