Not related to new protocol version, anyway:

if you delete in terminal chat logs from ~/.yappari/logs, yappary upon restart will put empty conversations always on top -> every time yappari starts, updates last date/time in empty conversations using current system time.

Dunno how to resolve (I think last date/time comes from chat logs), maybe last date/time for empty conversations could be taken from oldest date/time in non-empty conversations (works with at least one non-empty conversation).

Btw it's not a critical issue