Theoretically, if your IR interface is transparent to the COM port, you should be able to do File Linking across it in the same manner as you would across the serial port with cable. If anything works, everything should work.
You must set the preferences for each of the individual functions of "File Link Options" in addition to those of "File Transfer", "Modem Options", and "Page Send/Receive Options" by using the "Connect" button in Preferences on the PDA.
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