I used to have that misaligned disc issue with old quick release hubs. The problem went away with DTSwiss hubs so I figured out that the locknuts on the older disc hubs weren’t square with the opposite side. Back in the rim brake days it wasn't an issue. My solution was to mark the dropout and hub locknut so that the hub went back in the same orientation as when I aligned the discs. Newer better built hubs did not have the problem.
Feb. 20, 2020, 1 p.m. - Andy Eunson
I used to have that misaligned disc issue with old quick release hubs. The problem went away with DTSwiss hubs so I figured out that the locknuts on the older disc hubs weren’t square with the opposite side. Back in the rim brake days it wasn't an issue. My solution was to mark the dropout and hub locknut so that the hub went back in the same orientation as when I aligned the discs. Newer better built hubs did not have the problem.