Depending on the situation, you MUST accept the FSDT Live Update to overwrite your AFCAD, since it's not possible to know from which version you started with.
This might not usually a problem but, with the recent release of P3D V5, we had to update almost all our AFCADs, because the default scenery has been updated so, if you use P3D V5 and don't install the new AFCAD, you'll see lots of duplicated objects, missing objects, conflicts with default, etc.
So, you can do it but, be aware of the possible issues.