Hi! There's no need to edit file names in any way. The only thing that will affect how you call notes with suffixes is aliases.
If you're trying to combine multipitch banks, the pitches must match up. Is that the case with Gahata Meiji's bank? For example, every voicebank has G3, C4, F4, etc. If any of the pitches aren't the same, they won't align anymore.
This is what I think the original folder structure is like.
Voicebank 1
Pitch 1
Pitch 2
Pitch 3
Voicebank 2
Pitch 1
Pitch 2
Pitch 3
etc.
To combine them, you must restructure the folders like this.
Voicebank
VB 1 Pitch 1
VB 1 Pitch 2
VB 1 Pitch 3
VB 2 Pitch 1
VB 2 Pitch 2
VB 2 Pitch 3
UTAU cannot read more than one folder deep.
In each multipitch voicebank, there is a file named "prefix.map" that matches each recorded pitch of samples to music notes in the piano roll. If all the pitches are the same for each voicebank, you can simply use one prefix map for all of them in the main folder. But in order to use prefix.map together with suffixes for expressions, the pitch suffix must come after the expression suffix.
Edit one oto.ini at a time. Let's say that you're editing the A3 pitch of a soft voicebank. When you open the oto.ini as text, such as using Notepad, it will look something like this.
filename.wav,a かA3,500,150,-600,100,50
Go to Find + Replace. You can usually reach this with Ctrl+F or Ctrl+H. In Find, put the current suffix, "A3". In Replace, put the suffix you want to have, and the pitch, like "SA3". Do this for each folder. If you don't want an extra suffix, leave it alone, with the pitch suffix.
Then, each of the folders will have a suffix like: SA3, SC4, SF4, A3, C4, F4, PA3, PC4, PF4
When you use the voicebank in UTAU, you'll do things like [kaS][e][ru][noP][ u ][ta][ga]. Because of the prefix map, UTAU will actually look for files aliased with names like [kaSA3][ruC4][noPF4] etc. according to what pitch that note is on. And because we set up the OTO to include pitch suffixes, each of the pitches will still be called normally.
Good luck!