When we say a voicebank is "Encoded" on Kana or Romaji we mean about the files itself.
When you post you have both I can imagine you will be having 2 VB with the same samples but different names. I think what you want to say is a "Voicebank encoded in Romaji and Kana Aliased" which would work perfectly in UTAU.
Please tell me which one are you going for.
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I wanted to say that the VB is in Hiragana, but aliased in Romaji. Thanks for the notice, I have correct the mistake.
- Hikari~Hanabi