Hi,
Read All before doing anything !!!
iChat (the app before Messages) used to be able to Save Chats and these became the Archive folder.
It was thought for a long time that these worked independently from the ~/Library/Messages chat.db items (There are three here).
However it seems that the chat.db items also hold the info about the "recent Chats" as it were and an index of the archive folder that can link all the old chats together.
Some people have found that the ~/Library/Messages folder also has some *Incompatible* named items that appear to be dated to the last Update.
It appears these may have the older info.
I have seen one help site (that I also lost the URL for) that used the Terminal to merge them back together.
However it relieved on a specific point in time when the backbone of th OS (Darwin) had a specific version number.
EDIT Found it https://gist.github.com/nschum/1cf00aee2f1ac8869df4
Whilst I have not lost all the current ones I have updated beyond Darwin 14 as in the merge Script despite my folder looking like theirs.
Hopefully just changing the the Darwin version line would be enough to make this work.
I have not tried it myself yet.
Whilst it looks simple there are questions I have about it until I do and therefore I would not recommend it.
The other point is that it does not directly address the issue you have.
You have new chats "Missing".
Go to the ~/Library/Messages Folder (Use the Go Menu in any Finder Window whilst holding down the ALT key and select Library then Navigate).
Using the View Menu > Show View Options display the Modified Column (I use Cover Flow)
Does the date match up with the last Chat ?
If it does not new info may not be being written to this file(s)
Do a Get Info on the file(s) (CMD + i Keys)
At the bottom you should have Read and Write Permissions.
If you highlight your Name then Unlock the Padlock And then use the cogwheel icon you should see if your Own It (the statement should be greyed out).
Check the other two files as well.
9:17 p.m. Wednesday; June 24, 2015
iMac 2.5Ghz i5 2011 (Mavericks 10.9)
G4/1GhzDual MDD (Leopard 10.5.8)
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Mac OS X (10.6.8),
Couple of iPhones and an iPad