This has happened on 2 different drones, 2 different mapping missions, and 2 different Ipads -  we pause to change batteries - then select "resume" and it skips to the next way point leaving a gap in the mission.   You don't realize it till you get back to the office as the line grays out like it has completed.  It's hard to tell in the field where it's picking up if it's far away from you.
Had nothing but problems lately with the app in general.  We get radius errors where the drone takes off and just hovers and won't go to the waypoint.  

sometimes it will not resume at all after changing batteries and we have to exit the app completely, then it will transmit the data.

What do you do for app support? Or is there any?

Here is an example of where it leaves the gap

I have had this same problem on multiple mapping missions.  I've gone through manuals intensively looking for a way to create a break point before returning home for a battery change, as when it enters Auto return home mode, as you said the resume point becomes the end of the last vector.  

My solution is to wait until it reaches the end of a long vector and as soon as it turns , I hit the return to home button.  This way you minimise data loss.

We usually add extra waypoint in the middle of lines in case we have to return home for batteries.  and I know there are always waypoints at the end of each line.  But it's even done it at the ends, after a turn - the line grays out like it is complete, then it skips to the next one.  In my screenshot above, there was a waypoint where we ended, and it should have restarted the mission at the same waypoint.  But it did not, it skipped to the next one.  
GS Pro is honestly a big piece of crap with absolutely no support and an outdated manual.