Vw has put the brakes on payouts, thier hoping for a better deal under the trump admistration.
The Trump administration is not going to be able to do anything to this process. It is in federal court, which is the purview of the judiciary, separate branch. Even if the new administration's EPA director disagrees with the past administration's enforcement policies, there are other parties to this settlement whose interests remain, private claimants and state government (notably California) claimants. It is worth noting that the nominee for EPA director, the former AG of Oklahoma with a history of suing the EPA, has opined that states have primacy in determining environmental policy (they do now, sort of, in that they can impose stricter standards for emissions than the federal standard, but they cannot replace federal standards with more lenient emissions standards.)
The check issued is a result of a settlement offer made and accepted. Unless VW can show cause for stopping payment, then the seller has cause for action against VW, for civil fraud, bad faith breach and other wrongs.