I have a similar issue. I create a new layout from previously created layout template file with two map frames, then I want to point the keymap map frame to an existing keymap, I don't want them duplicated. Doing so, my legend is gone respectively not anymore formatted and with configuration gone.
Same thing happens if I change a property (for example changing a background). It always ends with having my legend(s) screwed up. Any solution or is it fixed with a newer version?
I use ArcGIS Pro 2.2.4 (unfortunately an update to ArcGIS Pro 2.3.x is not yet rolled out within the organisation).