I played my conference opener last night in my online dynasty. It also happens to be a player vs player match-up.
I was winning big and wanted to put my second team in for the 4th quarter. Partially because I think, even if you don't immediately see a change, it helps in the off-season with the training of your players, but mostly because I don't want any of my starters getting hurt in slop time.
However, when I paused the match-up, I didn't see a mass subs option any where in the pause menu like it is for player vs cpu match-ups.
I subbed out my HB manually, but didn't want to make my opponent wait for me to sub everyone out. Fortunately no one got hurt (except the fifth WR on a special teams play, but was only till end of game).