Thanks for this report and my apologies. I am glad this didn't cause you to lose any of your improvements!
This was caused by the last update. The settings modal adds two submit buttons. The advanced city manager page actually loads the individual city's page that you are changing into an invisible iframe on the bottom of the page. Based on what button you click on the city manger page the script is told to click a button on the city page that is loaded in the iframe. Since the game's html is not very good about having any specific ids or other identifiable info I have to go by the order of the submit buttons in the html. The settings modal update changed the place of the improvement submit buttons by 2.
This has now been fixed and thanks again for letting me know!