Hiya! I've actually written notes about handling multipitch in both the voicebank creation and the voicebank usage tutorials.
FOR MULTIPITCH: In the main voicebank folder, there must be a pitch that has no suffixes in the OTO. All other pitches with suffixes should be in their own subfolders. Don't add suffixes to the file names, or else the index.csv will be incompatible.
FOR MULTIPITCH: If the voicebank you're using is multipitch, there are issues with Arpasing Assistant. The best thing to do is to temporarily remove all pitches with suffixes from the voicebank. The pitch without a suffix should be the only one remaining, and should not be inside a subfolder. Then, run Arpasing Assistant as usual. Once the UST has been converted, put the other pitches back in.
If you have a prefix map set up, the voicebank will work as normal once you put the other pitches back into the bank.
Arpasing Assistant refuses to work when there isn't anything in the main folder (that is, if everything is in subfolders). If you have every pitch of the bank in the main folder, with suffixes, and you don't remove them from the bank before running the assistant, then the plugin will choose samples from random pitches and you'll have to go through and remove all the random suffixes by hand.