Failed mission upload can result in waypoints from previous mission remaining

I experienced an issue last Thursday whilst doing mapping flights, the first 2 flights completed as normal however the third somehow managed to complete 121 waypoints out of a total 187 and then proceeded to head off in the direction of the previous mission. RTL was invoked and the plane brought home and landed. When looking at the BIN file the waypoints were those of the previous mission. I'm left confused as to what happened during flight 3. There were a couple of failed waypoint uploads on an earlier flight in the day and whether this is related or not I'm not sure. I have put the tlog and Bin's in a dropbox folder . The 2 logs to look at are 2016-05-05 14-39-35 & BIN442. The mission previous to this (the one that the plane reverted to after WP121) are 2016-05-05-13-03-31 & BIN441

https://www.dropbox.com/sh/fm5wozoec9u2dz4/AAAADlixI6Pcsizno5SWkBDva?dl=0

This issue was started in https://github.com/ArduPilot/ardupilot/issues/3338

Start by reviewing the linked ArduPilot issue #3338 and the supplied telemetry and BIN files, especially 2016-05-05 14-39-35, BIN442, 2016-05-05-13-03-31, and BIN441. Determine whether the failed upload explains the switch to the previous mission; done means the cause is identified and a reproducible fix or clearly documented resolution is established.

Written by the indexing model from the issue text.