There will be some bugs to work out of the system, but I would guess you will be fine with hopping on board a stop or two later. There have been times where I've been 2.5 hours into a 3 hour trip before the conductor made it to my car to lift tickets!

I'll bet the app has a means to override if an exception is presented. More of a concern is if your next segment or remainder of your ticket gets canceled! Another reason to break tickets up into one-ways when not cost restricted.