The majority of my imaging in EKOS has been by setting up a camera sequence, performing a focus, plate solve, start guiding, then run the sequence. This has been fairly successful until I lose the guide star for some reason (either clouds, or trees get in the way). Then it never attempts to go to the object again, plate solve, and resume.
So I decided to start using the scheduler. Picked my target, and I encounter the exact same issues repeatedly over the night for various reasons. Either a wind gust sets it off a tiny bit, or clouds interrupt guiding, but in either case, the original guide start is not reacquired, a new goto with plate solve isn't done, and over time, I'm no longer imaging the original object (or it's no longer centered). Also, for some reason when using the scheduler, the meridian flip isn't happening. I've had to force it to flip but sending a goto command.
Aside from the above issues. The scheduler state really gets screwed up when you need to interrupt it. If for instance, I need to pause the scheduler, and submit a goto command to get back on the object, then resume the scheduler, it will mess up the sequence. My sequence is Lx5, Rx3, Gx3, Bx3, and repeat until dawn. So, when I pause the scheduler because it's off the target and submit a goto command, then resume the scheduler. It might have completed L and R filters. For the rest of the night, it will only capture G and B, because it thinks L and are are finished, and it doesn't loop back to the beginning of the sequence.
What I've had to do to fix these issues, is to quit out of EKOS. Relaunch it, and restart the scheduler from scratch. I also have to rename the folder it was saving into, so that it will create a new folder. Some times it seems there is some residual hold over issues if I keep the first batch of files in the directory. I could be wrong about that last part, but I think at least once or twice it caused an issue.