I swapped out dumbbell chest press for bench press on my first exercise yesterday.  No issues saving the rest of my workout on my iPhone.

No problem, make sure you hit "finish exercise"

From what I know, you've got 2 options currently. 

1. Build your own custom workout.

2. Do the recommended workout, and instead of doing the exercise your talking about, back out to the home screen, go to exercises, pick the one you want, and do it!!

When your done with it, go back to your workout.  It will save it all the same.

I do this quite regularly, a more streamlined process would be great!

Nope, that answers my question.  I did have to go back into my history and delete the 4 extra sets. 

Question...what do you recommend in the scenario above. When you know you can't do the recommended sets/reps, drop weight and get the reps, or keep the weight and fewer reps??

I'm not really sure exactly what your asking, but for me personally...if I'm out of town, or had to work really late, and I have to skip the gym, I just pick up the next day where I left off.

Haven't had any issues on iOS

Will the app automatically change our workouts after a set amount of time?  

The back button definitely makes it easier to navigate, just wish it wouldn't delete the sets you've done so far, when you back out.

Yes, all of those. But I suppose if there's a back button(which I know is coming), that would make it easier as well. Sometimes, I have to plan ahead when the gym is busier. As it is right now, if I back out of an exercise via the home button, I lose my saved sets if I haven't "finished" the exercise.