As long as you can keep the original parts after the lowering you should be able to set it back to stock. Provided there was no cutting involved in the modification. Make you you do a lot of research on the lowering kit you intend to use to see what is going to be required.
Along with what Brider said another thing that may change is lean angle. That is going to depend on how much the bike is lowered….though with a sport bike that will be minimal.