I am definitely seeing this as well, although I'm not sure if it really applies to everything. Rescaled tanks and engines however definitely retain some of their properties on vessel save/reload, but forget others. Some behaviors that seem to happen 100% of the time include:
1) If make a stack of upscaled tanks and then save/reload it, detaching one of them will cause the attachment node on its parent to migrate inward to the place where it presumably would have been if it had not been rescaled. Anything you subsequently attach to that node will end up clipped into the parent tank, in the case of engines or engine plates so deeply that you can't select it anymore.
2) Up-scaled engines retain their upscaled size on save/reload, but then show in the staging display as still having their original, unrescaled thrust levels. If you launch before having done a save/reload on the vessel, the values show still correctly on the pad, but if you save/reload the game from that point, just like in the VAB they come back at their original default values.
3) When you reload a vessel with rescaled engines and then try to fix the problem by rescaling them again, the engines jump away from their attachment nodes so you have to translate them upwards to put them back in the right place. The re-rescaled engines will again keep their properties when you launch from the VAB, but again lose them if you save/reload your launch situation.