If the target was plate solved prior to the MF, then it should re-solve after it. So, if you're using the Scheduler and you tick "Align" then it will plate solve as part of start-up. When the MF happens, part of getting everything working again will be another plate-solve.
If you didn't plate solve before the flip, e.g. you just use the camera tab and Kstars planetarium to point at targets, then EKOS won't plate solve after the MF.
I have checked this several times. My sequencer runs always have the plate solving set for each task. When the flip occurs the current capture is aborted and restarted by no plate solve occurs. It has never done a plate solve after the flip.