The issue seems to be caused by the game using number of seconds since boot time for timing and converting it to a single precision float. An experiment of playing the mission during the time when number of seconds since boot crosses 2^20 mark seems to confirm the theory:

Notice how it becomes more laggy around 12 days, 3 hours, 16 minutes and 16 seconds of up time. That's because 12¤86400+3¤3600+16¤60+16=1048576, which is 2^20. The number of seconds took one more bit, which means the precision of fractional part halved.

A single precision float has only 23 bits of precision (not counting the sign bit), so if the number of seconds takes 20, we're left with only 3 bits for the fractional part. That's only 8 fps. Exactly as in the video.

Unless there's some other issue, rebooting the OS should help. For windows 8 or 10 it may be necessary to disable fast boot, to make sure the OS really reboots instead of pretending to do so.