Although we have never encountered something like this before (nothing that we know of can actually turn off the activesync on the server - syncs can fail but your server config should never change), i wonder if this has to do with the actual device ID reported by your device is different under different configurations. What exactly is the symptom that you observe ? Is there something you see on the server, or just sync failing ?
When the touchdown process is killed and restarted, and if you go into Diagnostic screen, there is a field on the top of the log where it shows the device ID. You might want to kill and restart touchdown and look at the diagnostics under different modes of the phone to make sure they show the same device ID. You might also want to write to support so they can investigate logging when the server calls fail.
thx!
-g