I'm with soundproof on this. Are you sure Marc you haven't just been un-plugging the BeoLab 2, and not disabling it in the BeoSystem 3 menu? Sorry if it seems like an obvious suggestion!
If the BeoSystem 3 still thinks it has a subwoofer connected to it when it doesn't, then it will be sending all the LFE content to a speaker that doesn't exist, it won't re-route to the BeoLab 5s automatically.
The BeoLab 5s should outperform the BeoLab 2 in absolutely every way. In fact, there's a good argument that using BeoLab 5s with a BeoLab 2 together would yield worse sound than using a BeoLab 2 with say, BeoLab 3s or 8000s. If the BeoSystem 3 really DOES send any bass to the BeoLab 5s, you could end up with some of the deep bass being cancelled out!