Because some of your bacteria resides on the sufrace layer of your sand, if you bury it in the rescaping process, some of it can be lost. In addition a healthy plant substrate if full of mulm. This is a mishmash of all the stuff that works it way into the substrate from fish poop to leftover food and dead plant matter etc. 100% of this stuff is never removed and what is left becomes mulm. So if you also stir this up it may break down some when back in the water/filter to the extent it is no longer buried nor completely removed.
So these two facts combined could result in a small, short lived rise in ammonia. However, this can be partly or completely mitigated if the result of the rescape is that there are more plants afterwards than beforehand. The added plant load may uptake any small increase in ammonia.
The odds that you will cause a serious bump in ammonia due to rescaping are not great in most cases. However, that does not mean they can't happen when one does major work on a well established, well stocked tank.
