Another "bug" seems to have crept back into the scheduler. Unfortunately, as I discovered last night, the logs were disabled by default in the nightly 3.3.8 Kstars version I was using last night. However, this has happened several times before, so Jasem probably knows how to fix it in a snap:
I programmed the scheduler last night, as you lined out above, using a fixed termination time for sequence 1 and a fixed start time, 5 min later, for sequence 2. That worked fine, as expected, sequence 2, i.e. Horsehead Nebula, started tracking aligning and exposing OK. Fortunately I woke up 22 exposures into that second sequence and quickly checked on progress. That's when it became clear that all 22 exposures were unusable as the guide module lost its guide star in ~ 10 s intervals. That also resulted in the image shifting out of center.
The reason most likely is that during the execution of sequence 1 a meridian flip occurred and the guide calibration was merely swapped instead of "recalibration forced upon pier side change". That swapped guide calibration was not reversed when sequence 2 started and the mount switched back to the other side of the meridian.
So, it looks to me that during one of the last updates the previously mandatory guiding recalibration upon pier side change was dropped. It would be great to have that option back in in the scheduler tab in Ekos.
It takes little time to recalibrate the guide module after a flip, but failure to do, as in this case, can easily ruin the image acquisition for the rest of the night.
Can this option be put back in, again, please?
Preferably, the 'calibration swap' routine could be taken out entirely, then this can't happen in the first place.