Continue with quick check:
1. If did you apply discount or did you post negative items, there should match also the VAT charges. That means, that VAT should equal zero as well. 100 EUR accomodation 10% VAT should be in opposite -100 EUR accomodation 10% VAT.
2. Is it deposite invoice linked to reservation and you system set-up requires final invoice. Then you should settle reservation.
Tip: If you don't want to create document with 0, set your HotelTime to not allowed raising an invoice with 0 value transactions.