I am playing/testing with a custom built app and doing session.addlap at 1KM intervals. What I have noticed is that the during the times when session.addlap is executed, the following will occur.
Scene1
1) the AutoLap notification screen will come up. (this is a "bug" and per input prev from connectIQ guys - this should not be happening). When the AutoLap notification screen comes up, a few things happen
2) the AutoLap screen will take over the entire custom app. If i were to press the ESC (Could also be any other key) to dismiss the notification (much like how one can dismiss a SMS notification by pressing Up/Dn arrow key), I would in-advertently exit the custom app.
3) in my custom app code, the ESC key is used to either exit the app (only if there is no current recording session in progress) or to add a lap. In this case, when the autolap notification comes on, pressing the ESC key will EXIT the app and present me w/ the "save/discard" NATIVE dialog box. (not the custom save/discard dialog box I created). In this screen, it will show up as 0:00:00 min and _:__km ran or such.
4) when I click save/discard - I believe (i didn't verify in detail) that a new recording session is saved/discared (my custom app activity recording however is SAVED, I think even before this NATIVE save/discard dialog box comes up
Scene2
5) I have also noticed that doing session.addlap and during the instance when the autolap screen comes up, GPS will turn off. (I think. need ConnectIQ guys to verify based on the FIT file from the link)
6) Why I say this - when I look at the MyGPSfiles rendition of the route, I can see that at the autolap locations (each 1Km), I will see that the track will "break" apart and then the GPS track after that could "struggle" to get another GPS lock and end up possibly a drunkard.
In the pic below - you can see the "breaks"

Here's the link to myGPSFiles
http://www.mygpsfiles.com/app/#8szaGkUg
Please let me know if this is a known issue or something to do w/ my code or something to do w/ the Resume Later bug
F3. FW 3.6 GPS 2.9