Harry, please aallow me ask some silly questions:
1.- Why going to BOBI 4.1 SP3 and not to the latest release?
2.- What are your constrains?
3.- How big in users/number of reports is your environment?
Perhaps meaning, can you spare a different hardware to install the new version? If your comapny can invest in hardware, then side-by-side installation could be set (as Jawahar mentioned) using different CMS; however is user number is big and you are using a standalone machine for Production and your productio machine is the same as your development box, etc, then performance wouldn't be that great.
I've seen many things and you can take different routes, it all depend what card you got under your sleve to play with.
Please share more info if need a deeper answer 
Regards
Reinaldo Nunez