Automatically detecting an encoding is not something that can be done accurately. It's pretty much essential that the encoding be specified explicitly. It can be guessed in some cases, but even then not with 100% certainty.
This documentation (Encoding) explains the situation in relation to Notepad++.
They also point out that the difficulty arises especially if the file has not been saved with a Byte Order Mark (BOM).
Given that your file displays correctly once you manually set the encoding, I would say there's nothing wrong with how you are generating and saving the file. The only thing you can check for is whether a BOM is being saved, which might improve the chances of Notepad++ being able to automatically detect the encoding.
It's worth noting that although it may help editors like Notepad++ identify the encoding more accurately, according to The Unicode Standard document, the BOM is not recommended.
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