Hi Aidan. We can start by considering your problems with Dec reversal after a meridian flip. Here's the explanation of that setting from the User Guide:
'Reverse Dec output after meridian flip' - tells PHD2 how to adjust the calibration data after a meridian flip. Some newer mounts track their 'side of pier' state and automatically reverse the direction of the declination motor after a meridian flip. Older mounts do not do this. In either case, PHD2 needs to know if the mount will automatically change its behavior based on side-of-pier. You may have difficulty finding information about how your mount behaves in this respect, so PHD2 provides the Meridian flip calibration tool to determine the correct setting automatically. It's also easy to figure out the setting manually with this quick experiment:
With the checkbox disabled, calibrate on one side of the pier, then move the mount to the other side.
If you are guiding via ASCOM or Indi or are using an 'aux mount' connection, just start guiding.
If you're guiding only via ST-4 and PHD2 has no scope pointing information, first select 'Flip Calibration' under the 'Tools' menu, and then start guiding.
In either case, if the guiding works normally, leave the box un-checked; but
If you see guiding run-away in declination, check the box and repeat the entire procedure, including calibration. You must repeat the procedure, simply checking the box doesn't "fix" anything.
Note: this procedure must be following in its entirety until you determine the correct setting. Changing the 'Reverse Dec' setting only determines what will happen in the future, at the next calibration.
So we implemented a tool for you to get this sorted out in the event you got wound around the axle (which you probably did). And PHD2 isn't "forgetting" your calibration, it is trying to force a new calibration because you changed the setting. If you are then literally restoring an older calibration, you're just shooting yourself in the foot. Bottom line, your mount almost certainly needs to have the 'Reverse' option checked - so check that box, re-calibrate, and you should be good to go with Dec corrections and meridian flipping. Also, don't start fiddling around with Dec guide mode being turned off or setting it to uni-directional, leave it alone on 'auto' until you get clear evidence that your mount has too much backlash in Declination.
In terms of your problems with high rates of star elongation, I don't think you've given us enough context to help. Elongated stars can come from source that have nothing to do with guiding or even mount tracking. For example, the 2.5 hour long guiding session you started shortly after midnight produced RA and Dec RMS values that were pretty close. Granted, the total guiding RMS was almost 2 arc-sec but that, alone, won't normally produce elongated stars. What is the image scale on your main camera? How long are the main camera exposures? What is the total weight of the payload riding on the mount? Can you post a photo showing an overall view of the mount, the payload on the mount, and cabling?
As you probably know the periodic error on your mount is very high with a periodic error over 50 arc-sec peak-peak:
The question is whether Sky Watcher thinks this is "perfectly fine". I can't say because this is an economy mount in the grand scheme of things and I don't see anything in the specs that talks about periodic error. So I would say your expectations should be pretty modest with this mount - usually meaning a very light payload and relative short exposure times with the main camera. By the way, PHD2 guiding managed to wrestle this periodic error down to less that 2 arc-sec peak-peak. If you want to help PPEC further improve on this, you should find the PPEC settings on the Algorithm tab of Advanced Settings and set the period length to 480 seconds and un-check the box for "Auto-adjust periodic length". Also, increase the predictive weight to 80.
If you intend to get into an extended period of trying to get more from the mount, you should start by following the attached procedure for get a measurement baseline of its performance. You should also update to the current 2.6.14 release of PHD2.
Good luck,
Bruce