Hi Noel thanks for the kind comments.
I never let the scope flip. I have automatic meridian flip turned off in EQMOD (in the Toolbox). My TS1506UNC f4 Newtonian scope on NEQ6 will track at least two hours past meridan at most declinations and I have the balance set so worm mesh is not affected much at the crossover point.
APT can reacquire. Sort of. In the latest versions (get the latest Beta, it's what I'm using)) you can script in a command to do a GoTo++ to recenter the target and it will automatically stop and start guiding (check box at bottom of Guide dialogue) for you as well. However I don't think there is any way of the script knowing the mount has reached the meridan so you would have to build a script which would take a number of subs before meridan is reached, script a GoToOffset or GoToAltAz (might be easier) to trigger a flip and then a GoTo++ to recentre the target based on the previous subs centre (orientation shouldn't matter). You could post a request on the APT forum Ideas topic asking if a meridian detection and conditionally running a script (you can branch scripts) could be added somehow. I think flips are best avoided though and generally will change target around the time it would be needed.
HTH
Duncan