@Morelli,
Thanks so much for documenting the system! We really need good doc of Ekos for all languages.
Wolfgang is the expert on this topic, meridian flips, but I'll take a shot at my understanding of what's going on to get you started. (I'll try my best--but please follow up if I don't respond to what you're looking for.)
Ekos, inside the mount module, regularly monitors the telescope position that your mount hardware broadcasts. If enabled, the mount module will try to initiate a meridian flip once the hour angle condition for a meridian flip is met. This condition is something like "mount on west side of pier, pointing east, and hour angle is positive by a specified amount, e.g. the parameters filled in on the mount tab". The mount module communicates with the capture module, so if, when the condition is met, and a capture is in-progress, it will wait until the end of that capture.
When the mount module is ready for a meridian flip, and capture is no longer busy, the capture module suspends guiding and tells the mount module to go ahead with the flip.
The slewing part of the meridian flip is really performed by the mount. That is, all Ekos (the mount module) does is issue a slew command to the target position. The target position is usually the current position of the mount give or take a little bit of dithering, guide error, and alignment error. It is basically the desired position from the previous slew. So, all Ekos does is issue a slew command to "the target position (RA/DEC)". It is the mount hardware, not Ekos, which should realize "the target position should really be pointed to from the other side of the pier", and should slew over there. Most meridian flip issues wind up being caused by this (e.g. the mount not realizing that the pier side should be changed, e.g. because it doesn't think it's near hour-angle=0, or because it has the wrong lat/lon, wrong time, etc). This is why we have meridian flip conditions of a certain margin past the meridian, to insure that a small difference between the mount's position understanding, and ekos' doesn't cause the meridian flip to fail.
When the meridian flip slew is done, and the mount seems to have changed pier sides, the capture module is in charge of resuming processing. It resumes guiding, if guiding was suspended -- i.e. if guiding wasn't running before the flip, it won't start guiding after the flip. It starts up an alignment for the target position. I don't believe there are any parameters that need to be set for it to resume guiding or start alignment. Once those things perform successfully, capture resumes its capture sequence.
Hy