Not following exactly what you you said or what your question is but...
If the pipe is pressurized, then nothing is keeping you from changing the elevation of buried pipe. Up, down, whatever you need to avoid conflicts.
If is is not pressurized, i.e. a gravity drain such as sanitary or storm drain, then you're a little more restricted in that as long as the flow goes DOWN in the direction of flow you're golden.
You do want to be mindful of any future structure that will be built above the pipe (foundation, driveway, road, etc) and not go too shallow, such structures can damage shallow piping. Conversly, going too deep gets costly.