I too have .iChat files going back to 2004.
The older ones (pre Mountain Lion) are still in the 'iChats" folder with the default Home Folder/Documents.
(I migrated an Leopard User Account to this iMac)
The New ones are stored in ~/Library/Messages/Archive by date or Session.
Today I sent an Bonjour IM from one of my other computers and then closed the chat.
The Session/Chat Save reads just the "hi" I sent.
The Chat in the Messages window showed the "history" to today's chat as well (made up of several older chats)
I am not seeing any of these older/previous chats having the Modified Date change to suggest they are being overwritten.
As far as I am aware Messages does not make a sort of "early" Save of any chat that is "open" in the Messages window that might explain a current "chat" being overwritten at Save.
I tend not to keep old conversation of chats open in the Messages window once the chat is Finished.
I have seen people post pics of loads of open chats down the left hand side.
I have not seen anyone post that they were "losing" any that they had open. Or any suggestion that there was a limit.
Reading this bit again
For example if I had four messages with someone at 10AM, and later talked with them at 11AM, Messages will overwrite the 10AM log with the 11AM log.
I restarted iChjat on my Snow Leopard MacBook Pro.
I sent a new Bonjour Message.
I have the Chat window on the Macbook Pro showing me I sent "hi" earlier as I did not close the window before quitting.
However on the iMac in Messages this "hi" is not show in the 'history".
Opening the "Saved Chat" the time of being Modified has changed and the "hi" has disappeared and thre new IM has been added (Overwritting as you say)
It show older "history"
Comparing the Snow Leopard/iChat 5 pic with the Messages Chat it is in shows the missing "hi" in the iChat 5 pic.
Also a Pic transfer failed so I resorted to sending via the Finder and then placed in in the chat for comparison (which is why it on the "wrong" side)
Also despite it looking like the pic was sent from the iMac to the MacBook Pro it actually also failed in this direction.
So I can replicate what you are saying - that after a Saved Chat has been created during that session of Messages, if the chat is closed and reopened the reopening overwrites the file. Any subsequent IMs are also added as they happen and not at "Close".
Same "Chat" opened from ~/Library/Messages/Archive directly
I am not sure what to suggest.
I have not tried using my three computers and the multiple Accounts I have to create many iMessages and Chats between them to see if I can replicate the losing of "old but Open chats" that you also suggest is happening.
It may be useful to know how many chats or iMessages you have listed in the list on the left when this sort of thing starts happening.
And how old a chat might be when you find this has happened.
Please, if posting Logs, do not post any Log info after the line "Binary Images for iChat"
iMac 2.5Ghz 5i 2011 (Mountain Lion 10.8.2)
G4/1GhzDual MDD (Leopard 10.5.8)
MacBookPro 2Gb (Snow Leopard 10.6.8)
Mac OS X (10.6.8),
Couple of iPhones and an iPad
"Limit the Logs to the Bits above Binary Images." No, Seriously