Here is an update. I did not have a lot of time to work on this. My build for ATmega256RFR2 seem to be broken (I think it is AS7 issue), so I used SAM R21, but logically they should be the same.
I also could not get HADemo to run (or react to serial input, anyway) for some unknown reason.
I used WSNDemo and it works properly by default. I suggest you try that on your hardware first.
On closer examination it looks like there is a parameter clearNeighborTable in the joinControl structure. It should be set properly by the default HADemo application as well, but it may be worth checking that it is actually set correctly.
I'll try to make HADemo work on R21, but I won't mess with my AS7 versions.
If nothing else helps, create myAtmel ticket, they may actually know about some issues and have a fix already.