I guess it's all down to individual garages and their levels of service and customer happiness to go back...So, it could be costly but with such an important job they will hopefully be some what caring??
Could be any number of things. After that work it could be a loose connector, immobiliser not disengaging, TDC, coil pack blah blah blah. Most of these would most likely show as a light but the garage will be able to sort.