Unfortunately diffing and merging is limited with blueprints. I think Perforce has some functionality for this, but I have not tested it myself. I try to mark most changes in a new version with a comment named after the new version.
You can search for these comments in blueprints to find most of the changes. However, I do not mark every minor change I make in such a fashion, so it is not perfect. It is possible to make updating to a new version simpler by not touching any of the core blueprints of the toolkit, but adding your changes to child actors of these blueprints. However, this can sometimes limit you in the sort of changes you can make, so it is unfortunately not ideal either.
The safest approach, and the one I would generally recommend, is to merge and copy over your own custom changes manually. However, this is of course time consuming, so you’ll have to consider whether the changes in the update are worth the hassle, or if it is better to keep working with the older version. I wish I had a better answer for this, but I’m afraid I’m not aware of any perfect solution for this.
I’m very sorry to hear that you had to bang your head against the wall for a week for this, Locoweed. This is something that I should clearly have discovered and fixed a long time ago, and I thank you for posting your solutions here. From your screenshots it seems like you are not using the latest version, though. My last update was a major overhaul of the turn system, which I had hoped would eliminate these sorts of issues (among other things). I am away now and cannot confirm for myself for another week, but I will certainly look into this when I’m back and see if this is still a problem. If so I will make sure to fix it.