Can manufactured countertops warp
The difference in height can be from 1) bad initial installation, 2) someone sitting on one of the panels, 3) warping of one panel, 

1) Leveling two pieces of plastic laminate (Formica, etc.) is mostly an “art” and patience. Yes, the initial installer could have given up after a few tries. 

2) Settlement...ugh...I cringe when my teenagers decide to “help” in the kitchen. An easy test to determine if this is the cause is to pry on the two pieces (gently) and see if they move independently from each other. 

3) I’d look under the counter and verify that both panels are particle board. We generally use plywood near sink installations. If it is plywood, it could continue warping with additional water splashed on it, change in humidity, etc. 

Here’s an article that explains: https://homeguides.sfgate.com/laminate-countertop-put-over-plywood-particleboard-99004.html

Removing and reinstalling the countertops is difficult because the base will be deformed from prying the tops loose. If the problem is truly just a difference in height, (and not that the two panels have twisted, rotated, moved out of “square”, etc.) then I’d try slowly raising one panel with wedges (shims).