Currently part way through my egr delete and fmic fitting. I’ve followed the guide in here and was wondering what happens to these two rubber hoses? Because if I remove everything then they will just be left to atmousphere

Do I just plumb one in to the other? 

Yes, they're full of coolant so venting to atmosphere probably not the best idea.

Yeah found that out so left it all in place! Will bypass it at a later date!