In sentence 1:
Espero que lo hayáis pasado fenomenal en Chile.
I hope that you had a great time in Chile.
we are using the expression "pasarlo bien" which means "to have a good time"; it is idiomatic as you can see, but if we translate it literally it'd be "to spend it well". That "it" would be the "lo".
Lo pasé genial en su fiesta de cumpleaños.
I had a good time at his birthday party.
Also note that this "lo·" is "la" in some Latin American countries, e.g.
¿La pasaste bien?
In sentence 2:
Esperamos que lo hayas terminado a tiempo.
We hope that you have finished it on time.
here "lo" is a direct object pronoun refering to something masculine singular. They could be talking about a project or an exam...
Esperamos que hayas terminado a tiempo tu proyecto/tu examen. -->>Esperamos que lo hayas terminado a tiempo.
I hope this clarified it for you.