They must be input into RPM or ProGrammer in correct logical channel number order.
Unless that was changed RECENTLY in radio firmware and the programming software as well.
One of the first things you learn about programming a Harris (whatever...so many brand names in its history) radio is that the LCN order has to be right or you miss calls.
Motorola's radios all worked off a standardized frequency table. For example. 866.0125 might be called channel 801 in the table. The trunking controller would issue a command "Talkgroup 123, go to channel 801" in its language, and the radio has the channel table in it so it goes to the right freqency.
EDACS is different. The controller says "Talkgroup 123, go to the fourth channel in your frequency list" but that frequency list is the one that the programmer entered into RPM or ProGrammer. Neither the trunked controller nor the radio refers to a frequency table.