Hi Oscar,
I will try to help ... Sorry if my english is not so fluent sometimes.
Exactly the same happend to me ... the DataPilot was not resuming the mission after a battery change and like you, I am sure there was a time he continued the mission after a battery change automaticly. On Top, DataPilot crashed each time, when trying to sync a mission.
To get help I called Yuneec Germany ... It was a very pleasant and helpfull call.
Since the last Update there are some deep changes, that Yuneec does not mentioned
First of all they told me i have to remove the flightmode app, since this app is for the H+, runs in the background, interferes with the DataPilot and is responsible for the crasching ... So, remove it. If there ist no flightmode app on your st16+ .... ok. thats good ... Just go on with the next step.
Second if you call the H520 back (RTL, Manual or automatic) and you get the promt "Leave Mission on vehicle, Remove Mission from Vehicle, Resume Mission from Waypoint Nr. .... " select "Resume Mission from Waypoint Nr. ...." ..... after a while he will show you the Mission with the remaining Waypoints. Anyway wait for a shor time. Now you can Power off the H520 and change the battery .... the DataPilot maybe restarting now .... thats ok.
After changing the battery, Power on the H520 and now be patient .... Wait till the H520 completely connected with the st16+ by itself ... that may take a while, but it happens.
Now he is exchanging informations with the st16+ about the last mission. When this process is completed, the st16+ will ask you if you will start the mission. Thats correct. in contrast to earliere version the mission with the remaining waypoints is a "NEW" Mission for him. Therefor the Question "Will you start the Mission" (Theres no Question "Will you Resume the Mission" after a battery change anymore)
Same procedure after the second and so on batteries ....
To solve this problem it costs me two days and several calls to yuneec.
I hope I could help ....
Greetings Marc