When the client enters the network configuration phase after receiving a ClientboundStartConfigurationPacket, all sent and received chat/system messages are lost.
Cause
This is caused by Minecraft#clearClientLevel() calling Gui#onDisconnected(), which clears all chat messages.
Some other thoughts
This could also be working as intended, but I don't think chat messages should be completely gone when entering configuration phase, while still being on the same server.
There could also be a problem with signed chat messages, because the last seen messages are also being reset when switching packet listeners. Still, system messages have no signature and I don't see a reason not to keep them.
This is very annoying and currently convinces me to rip out the config phase. Maybe add a packet or something to clear the chat instead of doing it every time?