If you can correctly see your Thai characters when opening the book in the calibre Viewer then I think your book is probably coded correctly.
It's more likely that you're trying to read the book on the Kobo using a font which doesn't contain the necessary Thai characters.
If you've cycled through the whole list of built-in Kobo fonts and none of them are successful then you need to find a Thai-supported font-family from somewhere else (your PC, maybe) and copy those to your Kobo.
They have to be copied to a directory called fonts created in the root directory of your Kobo. After you've copied them you'll probably need to do a full power cycle to get the Kobo to "see" them. The new Thai font name will be added to the standard Kobo font pop-up accessed via the 'Aa' icon in the footer.
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