[RichH]

A good possibility is that the original repair was 'rushed' when the rudder was initially barrier/epoxy coated ---- what you probably see at the exposed surface of the HUGE section that is 'flaking off'.
Probably what happened is that the yard, etc. did not remove the amine blush that normally comes to the surface of an epoxy barrier 'coating'; they didn't use HOT water and then scrub the 'blush' away; nor, did they adequately sand down with 60-80 grit paper into the new epoxy to provide 'tooth' to enhance the adhesion of the successive layers.
Another possibility could be also be that they attempted to 'hot coat' all the 'layers' together - Applying and not letting each layer fully cure before the application of the next component layer and then expecting each successive coat to bond with each other. Such 'hot-coating' sometimes works; sometimes it doesn't work with respect to adhesion of all the successive layers depending on how fast or how slow the intermediate layers take to 'cure' ..... and if there is generation of the normal amine blush from the preceding epoxy layer.

So, ...... If the surface of the this (barrier coat?) epoxy layer is still intact, not blistered nor cracked .... and the yard needs to immediately launch this boat ..... Id just 'slop on' some bottom paint and then later do a correct repair later-on when the boat is hauled.
However, If there is evidence of water intrusion into the rudder, then an immediate complete repair should be considered ..... BUT, if the rudder is water-logged, it will take some TIME for the rudder to dry out before you can do a proper repair.

IMO - slop on some bottom paint now; and, do a thorough repair job when you have the proper amount of available time to do so.