This is most likely because a wrong combination of the BITS/BITS2 and AltSigWhenReleased/AltSigWhenRepeat/AltSigWhenRepressed and RepeatSignal is used.
In my tests during development, I have had this happen many many times, but I have never had problems getting the remote back on track again..
Here is how to get it back again.
Opening the remote is not difficult, but you need a small torx screwdriver, Beoworld has a fantastisk description off how to do it here. Opening the remote is totally your own responsibility !
After getting your remote back on track again, then upload a new configuration with the FIXED values in the XML file, don't try the "It might work this time" approach, as this will again crash the remote.
The first step to fix the problem in the XML files, is by setting the value for RepeatSignal=0 and removing any "AltSig...." occurences in the XML in the IR section.. The problem is most likely caused by a combination of these values..