KGB, no the fix should not affect already sent units.
When a unit is sent (i.e. teleported) it is already created in the armytable in database and has a destination etc.
My fix only affected the city-settings, i.e. do not try to send next produced unit to another city. So it should not affect. Then again, stranger things have happened
Let me know the gamename and city names of sending / receiving city and I´ll check.
Maybe your pegasi wasnt in transit already, maybe you only saw that the receiving city was receiving production from your sending city (but nothing was in transit yet) before you stopped the vector?