Sometimes I can't edit text, if I want to edit it I can highlight and delete/copy and paste; after a while it works but I don't know why/how. (this problem happens for all of the text editing, where I can't edit the code in the code module or the dialog in the dialog module); it may happen due to me liking to put the application in fullscreen? Otherwise I don't know why it happens.
Also you may want to look at how Sand: A Superfluous Game works with prefabs! I think it is made in Game Maker so it may not translate 1:1, but it does have a discord server that you may want to join to talk to the coder (if he also has the time of course) about having stuff translate between updates