it matters what sysnand your running in regards to 6.x encrypted saves, if your sysnand is on 6.x+ and you use the web exploit, your existing 6.x saves will work in classic mode, if you downgrade to 4.x your 6.x encrypted saves will not work.....emunand version doesn't change it
works the other way around too, if you have a game that uses 6.x save encryption (such as MH4) and start it in classic mode while sysnand is on 4.x, if you try to run that cart in a 6.x+ sysnand console the save will also be considered corrupt