Could you please upload the .log files to see if this is an issue on our side or there is something unexpected going on after the battery warning is triggered. Make sure to indicate the date and hour of the mission so we are able to investigate the corresponding events in the file. More information here: (Android, iOS) How to extract the log files.
@Nathan and @Soil, could you confirm that you received the battery warning before clicking the Pause button? Did you maybe have the chance to try the “It works perfectly when I pause the flight before the warning” workflow? Do you experience the same issue?
As a side note, gaps in the image acquisition can happen because of connection loss with the Fast mode. To know if the drone regularly took pictures, we suggest that you open Pix4D Desktop on your computer and import the images that were saved onto the drone (SD card or internal memory). The images have accurate coordinates but not the icon on the Map view of the app.
Best,