Have been using MapStruct version 1.3.3.Final and did not have an issue.
After changing to version 1.5.5.Final things start to fall apart.
Checked the generated implementation file after “mvn clean install” and realized that not all properties are inherited, could not figure out why or any pattern.

Below is a simplified example of what was being used.
The actual setup have multiple layers of inheritance.
Appreciate some clues and guidance here.

@Mappings({
  @Mapping(source = "incomingPayment.currency" target = "currency"
  @Mapping(source = "incomingPayment.debtorAccount" target = "debtorAccount"
  @Mapping(source = "incomingPayment.debtorAlias" target = "debtorAlias"
})
Payment mapIncomingPayment(IncomingPayment incomingPayment);

@InheritConfiguration(name = "mapIncomingPayment")
@Mappings({
  @Mapping(source = "incomingPayment.amt" target = "amt")
})
Payment mapIncomingUSDPayment(IncomingPayment incomingPayment);