Firstly lets clarify some things:
Messenger Plus! is an addon to Windows Live Messenger. Messenger Plus! only logs the conversation; the conversation is not sent through Messenger Plus!.
If you have Vista there is a feature called Shadow Copy. This creates a backup of the file so that you can rollback changes. This will only work if System Restore is enabled. To get here you need to right click the file and click Properties then the Previous Versions tab.
Other than that there isn't really a way of telling if the file has been altered because Messenger Plus! logs the conversation in real time. Therefore the last modified date is going to be constantly changing.
Simply put if she has no way to prove it than she has no case. I say believe your son. He openly let you read his chat logs. Also if these files are encrypted by Messenger Plus! (meaning you need a password to view them) they cannot be altered. Any manual change can render the file unreadable.