Well, I haven't heard anyone getting banned from PS Vita trophies. However, my method is pretty simple.
Make sure that you have all homebrew closed and not open, then I just log into my account, have the folders already in this directory: ur0 > user > 00 > trophy.
I usually would suggest don't put an account you care about if you want to be 100% sure that you won't get banned.
Hopefully this helps you.
There's no complex method like people make it out to be. Make sure you are signed out when using MolecularShell/Vitashell or any Account Switchers. Make sure your trophy folders are in the correct place, load the trophy app and let them rebuild. You can now sign in and sync the trophies, be sure all homebrew are closed.