(adsbygoogle = window.adsbygoogle || []).push({}); So, an account it's trophy hackable, but has trophys obtained legit, if I wanted to carry out the trophy modding on the account would the those obtained legit trophy would have to be synced before carrying out the trophy modding.
The legit obtained trophys are different to the ones that are in the folders of platinums ready to be used on the account.

You'd get d55, but your new folder (of the same game) won't sync unless it has a newer dlc or older timestamps.

(No different games entirely.)
Say it has 5 games of trophys those don't have to be synced before carrying out the trophy folders?

If they're already on the account, you don't need to sync them.

So once I've synced all 100 platinums and it comes to the sync which goes to 100% on the percentage bar. That isn't required to go all the way to 100% or ?
If I want to go to 100* that final sync isn't needed and will only slow down going to 100* trophy level.

No, once you're past all the d55 errors, you can quit out. Waiting for 100% is both tedious and time-wasting.

What about all the ski folders that are left after the user has synced the platinums. Is it best to delete them to speed up processes or leave them be.?

SKE/SKI just means they successfully synced. You can delete them if you want.