His time created an alternate universe when traveling back in time so when he goes back it locks onto his timeline/universe it's explained in better detail in the history of trunks dbz movie

Yes, Goku in Future Trunks' timeline had died of the heart virus that ravaged him.

You have to go back through the Future machine to reach your future self in the repaired timeline. Make your way to "your" sky home in 2059. This is where you get your medallion, from your "future self".

(see the related solution question)

Yes, Goku in Future Trunks' timeline had died of the heart virus that ravaged him.

You can't delete Timeline. Once you change to it there is no going back.