Well, you're downgrading from 4.1 to 4.0, so you might lose some of the advanced functionality that came with 4.1. IIRC, the new password hashing was implemented as of 4.1, so unless the server was forced to use the old password hashing algorithm, you might need to use the [man]MySQLi[/man] extension on the 4.1 server. Don't quote me on that, though... my memory might be a bit rusty.
Why? Was there a specific quirk that you were experiencing/noticing?