Anyone with experience doing this in Phuket? I am about to do it and would like to know if it is done within the visit or have to wait till the following day to recover passport.

Immigration does not transfer visas.

They will only transfer entry/permit to stay stamps, extension stamps and do a annotation with info about your old passport and the last visa you used for entry.

If I recall correctly Phuket like most offices will do it on the same day you request it.