The Apollo astronauts talked about that, going from multiple Gs to weightless and back to multiple Gs. I think that there is more throttle control with the Raptors now than they had with the F1 engines back then, so maybe less of an issue. Anyway, this time they kept three of the Booster Raptors running through staging.
The Booster has a more complicated problem, in that it turns 180 degrees immediately after staging before the boostback burn. I've seen some speculation about fuel sloshing around leading to some of the engines running dry.