The short and possibly unpleasant answer is: "Run NTP on that server!".

Of course you need a modified configuration to prevent clock adjustments originating from NTP. Maybe let's see an example (thanks to Marc Brett):

server 127.127.1.0
fudge  127.127.1.0 stratum 4
driftfile %windir%\ntp.drift
disable ntp

(Answer by Marc Brett) NTP works with up to 1000 seconds of offset, but when the error is "big", where big is defined as 128 ms (!), it will by default step the clock.

It is possible to tell it to always slew the clock though.

However, in your case I would suggest another possibly simpler method:[1]

An alternative solution suggests (I assume that there is a chance of simply taking the server offline for 30 minutes sometime during the next few weeks):

This answer provided by Vladimir Smotlacha was rephrased by the editor.

For example, the Linux implementation of the PPS API contains the echo feature for the serial ports. The principle is quite simple: An event on the DCD line causes the interrupt routine to generate an event also on the RTS line after getting the event's timestamp. With some external device like a two channel oscilloscope or counter one can measure difference between original signal and its echo. About the half of the time is the delay between creation of the event and getting its timestamp. That way one can estimate the delay and jitter between real PPS signal and its timestamps.

An utility named ppsctl (formerly named enable_pps) can be used to activate echo on a port by additionally specifying -eX, where X is either a (assert) or c (clear). The utility just sets the flags as described in [RFC 2783]. The Linux implementation will always clear the RTS bit in the UART if an event becomes active, and it will clear the bit when the DCD line changes back to the inactive state. Therefore you cannot have an echo for both events.