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I’m not an expert…but
I’ve worked with 4.0.x and 4.1.x version.
One problem I’ve encountered between those versions is the length of password encryption, you can find this
faq for more.
Secondly, a difference that I discovered was the language encoding.
If you have a site in 4.0.x and an ISO encoding you can easily modify the database records through the phpMyAdmin.
When I upgraded to 4.1.x, I couldn’t select the ISO encoding anymore (but the site was ok). One possible solution is to convert the site in utf encoding, this is fully compatible with mySQl 4.1.x
Anyway, that’s just everyday stories of madness – probably you should try it first locally at you pc and then go public.