The Reset Clock Seconds command (see page 21-6) can be executed from a macro triggered by a logic input.
First, create the macro:
MPW 20 9201 DD 48 3 * ; Reset Clock Seconds
Then, assign this macro to be executed when a logic input transitions from high to low:
MPW 26 0061 9201 * ; Assign macro to Logic In 1 Hi-to-Lo
If your controller has its serial port attached to a server, a script on a server can send the command over the serial port:
MPW 48 3 * ; Reset Clock Seconds