Looking at the PHD log, it looks like PHD lost the actual star, thought it found a different one but didn’t and kept sending max guide pulses until it found an actual star then continued guiding from there.
00:32:54.630 00.000 6356 ScheduleExposure(3000,3,1) exposurePending=0
00:32:54.631 00.001 6356 Enqueuing Expose request
00:32:54.632 00.001 6356 Alert: Your Max RA Duration setting is preventing PHD from making adequate corrections to keep the guide star locked. Increase the Max RA Duration setting to allow PHD2 to make the needed corrections.
00:32:54.987 00.355 6356 Resizing image to 485,363
00:32:55.379 00.392 2400 IsGuiding returns 19637768
00:32:55.379 00.000 2400 scope still moving after pulse duration time elapsed
00:32:55.530 00.151 2400 IsSlewing returns 945
00:32:55.546 00.016 2400 IsGuiding returns 1293618858
00:32:55.546 00.000 2400 scope move finished after 1995765714 + 1996657808 ms
00:32:55.546 00.000 2400 Move returns status 0, amount 1000
One night PHD2 lost the guide star while I was at the scope but it was not cloudy or anything. It looked as if the cameras exposure setting got change as the picture was very dim with few guide stars and gave me the same max duration warning, after a few minutes of this it started working properly again. Maybe the same thing happened here, I am using a ZWO 120mm guide camera.