Hi RSP – If your side-by-side apartments are separate Lots within your Strata Plan and you're talking about physically amalgamating those, then there's a lot of work involved including valuations and the preparation and lodgement of an Application for a Strata Sub-Division with the Land & Property Management Authority (in NSW).
I won't go into the detail now just in case your apartments are not as described, but otherwise post back to the Forum for further advice.