You should expect not only a period of adjustment when pitchers are promoted to AAA and encounter the ML ball - you should expect them to be less effective, as measured by ERA, WHIP, SLG against, etc. The fact that this ball has caused a spike in offense at the major league level (and the AAA level) indicates that pitchers are just less effective, as a group, with this ball.
Of course, that's not going to impact all pitchers the same way. My guess is that pitchers who depend on pinpoint location, on consistent breaking pitches, are likely to be in more trouble than flamethrowers, because this ball is slicker, harder to control consistently, and apparently doesn't break the same way as a result of spin even when controlled.
Probably the only way to evaluate pitchers in this environment is by comparison to the same season's league averages - season-to-season comparisons look to be pretty much useless, because the change in "environment" (e.g., the baseball) is evidently significant.