Can I use a Peugeot 206 1.6 55reg BSI unit in a 1.9 diesel s reg

No, they r completely different units & even if the wiring plugs match, u will never get it to work. Besides the BS l cannot be recoded to another engine ECU once it has been matched. So if it is a second hand BS l u will need to swap the engine ECU which will not work with ur engine, & if it is a new BS l it will simply never recognise ur engine, or dash panel, or airbag ecu. Further, a 55 reg BS l is a CAN-CAN interface & an s-reg 206 will be a very early VAN-CAN interface, so even the network protocols r totally different, including their bit-rate.

Even before u asked this question u obviously do not know enough about what would be involved to accomplish this even if the BS l could work!