Changing Primary Domain

[Aarias]

Hello,

I currently have two domains, the primary while the second one is currently parked. I would like to make the parked one my new primary and according to bluehost

(it) may cause some site files, scripts or other applications to break, requiring modification to work with the new site location.

I am trying to evaluate my risks upfront so do you happen to know what they mean by that and what I should do?

I do automatic backups so that shouldn't be a problem so based on your experience what else could go wrong and what files could be corrupted or break??

Thanks much in advance