Since there is no answer, I tried this myself.
Had 0.15.0.1 installed and working well, and did an install of 0.16.1 over the top.
All seems to be working, getting a couple freezes (not enough to worry about though), which I didn't have on 0.15.1, but it could just be bugs, or could be I'm doing something I wasn't on the previous version.
Using it for daily, pretty happy at the moment.
And I left the top a2sd selected, not sure if it would like me changing it after I already had apps moved with the one script.