As this ticket drove me nuts, a little description (as always 😄 ):

1. rollback problem - we have a bidirectional relationship between Transaction and Shipment. The problem there was that we were not assigning outgoingShipment to the Transaction instance, we were only doing it for one direction, so for shipment like:

shipmentInstance.addToOutgoingTransactions(debitTransaction)

For correct bidirectional relationships, we have to add it for both sides.
Grails is that clever, that when doing addToOutgoingTransactions, it was automatically assigning the outgoingShipment for the debitTransaction also, but it was not persisted. In grails 1 it was working due to OSIV, that was catching those "dirty" changes and here, it doesn't work, because we saved the debitTransaction a few lines above.

What also fixed the issue was removing this:

 if (!debitTransaction.save()) {
       log.info "debit transaction errors " + debitTransaction.errors
       throw new ValidationException("An error occurred while saving ${debitTransaction?.transactionType?.transactionCode} transaction", debitTransaction.errors)
}

because then, the debitTransaction was saved at the end of the session and the outgoingShipment set by the:

shipmentInstance.addToOutgoingTransactions(debitTransaction)

was caught.

We could either change it to validate() and let Grails do the work with associations, but I think the path I went with assigning it explicitly is a more proper solution.

2. quantity available not updating when deleting the shipment:

This drove me nuts.... since we were refreshing product availability asynchronously and the session that was deleting picklist items was not yet flushed and the productAvailabilityService was creating its own session and transaction, it didn't know "what is going on" in the first session, that is deleting the entities.... so it was thinking that picklist item is still in the DB (because the deletion was still in batch in first session)....
After long debugging it turned out, that we have missing properties for product availability jobs, which was the delay.....
Adding the delay, fixed the issue, because the first session "managed" to finish and to be flushed before the second session (from the job) initialized.