Nope, that storyline was always going to happen.
Remember, Prison Break started filming after season 1 of LoT.

I think it's when we heard Wentworth wasn't returning full time as series regular for season 2.

Dominic was one busy man that year of 2016, he had no break.

I think 2x08 of LoT is the first time you can see that Dominic face looks a bit beat up.
For Prison Break, you can see it in episode 5x09.

So I'm assuming LoT 2x08 & PB 5x09 was filming around the same time.