Auto-leveling micro-adjusts the relationship between two Z axis motors to ensure that the nozzle is a uniform height from the print bed at all points on the bed. Auto-leveling merely adjusts the first layer and has no effect on subsequent layers.
Why is auto-level necessary?
Two Z axis motors can not possibly be kept in sync with each other. As a print proceeds, the two motors drift out of sync and lift each side different heights, causing the X axis to become un-level with the print bed. If two Z axis motos could be kept in sync, they would be, and you would need to auto-level your printer only once during it's lifetime. That is certainly not the case.
Auto-level simply masks a deeper problem.
The X axis must be auto-leveled at the start of each print job. Indeed, the amount of adjustment necessary at the start of a new print job is exactly how unlevel the X axis drifted to by the top of the previous print job. Auto-level simply compensates for the underlying problem on the first layer, it does not attempt to solve the basic underlying problem.
Eliminate the problem
Use only one Z axis motor, synchronizing both Z axis screws with a timing belt. That way, you only level the X axis with the print bed once over the lifetime of the printer. And, with no variation between Z screws, you also get level layers over the lifetime of the printer all the way to the top of every print job.