Audio snap is a very powerful tool if executed correctly. It sounds like you are just moving a couple of transients slightly.
It has two mix engines … one for “on line” rendering and one for “off-line” rendering. The on-line or on the fly rendering is intended to give you an idea of what it will sound like. There will be hiccups in it.
When you are satisfied with how you have moved the transient either bounce the track or export the track … at that point it will utilize the izotope algorithm.
Unless you have other issues, if you are just nudging things around a little bit it should be seamless.