When they replace the motherboard your console might already be banned (the new motherboard may already be banned)
You should seperate your profiles between hacked and retail so that you avoid any traces of the hacked software, for instance, F3 don't work/exist for Retail consoles... if they see that in your profile you are likely to get a ban...
It's logical that they write the original nand to the motherboard's nand by default yes... unless of course you asked for something else...
The DVD Drive should probably be kept with OFW to avoid ban as much as possible, because... even if it's safe now (haven't heard of anyone beeing banned for ages due to having a flashed dvd) at any moment microsoft might start mass banning flashed consoles...
The best solution for Online + Hacked is 2 consoles, that way you are as safe as you can be...