also, you probably also want to send one block of zero's in to clear the audio buffer before switching, so i think it's generally a good idea to have 2-3 blocks of headroom between the line down time and the block switch.
Thanks for your reply, can you tell me how to do this?
Also in case you're wondering, I'm using RJDJ's libpd for iOS, so there's no GUI.
Even if no GUI is displayed, I believe that gui objects within the patch can still be processed. I would recommend making sure that there are no updating GUIs in your patch.
Can you attach your patch so we can see what you're doing?
Also, are you sure you're achieving a block size of 16? The default in libpd is 64, and while you might request a specific block size, there is no certainty that iOS will provide it - especially running at 44.1