While the application itself has been renamed, the mimetype that gets added to the system is still riot:
https://dev.getsol.us/source/element/browse/master/files/element.desktop$10

MimeType=x-scheme-handler/riot;

This just needs to be updated to:

MimeType=x-scheme-handler/element;

A temporary fix is to edit ~/.config/mimeapps.list and add:

x-scheme-handler/element=element.desktop

@silke you will be interested in this. :)