The additional - and 2 digits at the end of the violations is known as a "Ticket PIN". I may look like it's part of the ticket number, but it's not. It's only used as a password for the ticket when appealing it.
As an example when creating a violation, it appeared as: 2-001017-12. The actual internal ticket number is 2-001017, same format as it has always been. If you search violation 2-001017 in violation search it will appear as 2-001017. Additionally if someone did type in the ticket number and PIN (2-001017-12) it would return the same ticket.
This means the reports in the FTP file for example will only reference 4-001234 as the ticket number, not the additional -12.
Additionally, the code that generates the FTP files isn't going to change/add the pin.
FTP reports will remain unchanged by the addition of the violation PIN. No PIN will be shown in the mailed out violation.
The PIN is only used when appealing tickets if the user isn't logged in (this functionality is used on the new PHP user side, Brown is currently using the old ARO user code, so you don't see the new appeal area).
As an example you can see the "Appealing a Ticket" box on the log in screen here. The pin is used in that box to give some protection from public users just looking up sequential ticket numbers.