Shortcodes and html not working after latest WP update

I'm hoping the community here can give me some advice. The latest WP update to the shortcode api caused a major feature on my site to break, here is a description of the issue:

https://make.wordpress.org/core/2015/07/23/changes-to-the-shortcode-api/

I use a plugin called Custom Content Shortcode that pulls in resources by taxonomy and links to the post. The plugin author is aware of the issue, but I do not have a fix as of yet. If you see the sidebar on my page, you see that all of the links are looping to the current page, instead of the resource. This is because WP changed the way shortcodes and html work:

http://sbccimplementationkits.org/demandrmnch/fp-overview/

I'm looking for any advice or examples on how I can restructure this to work within the new WP update. Here is the code that it uses:

[loop type="ikitresources" tag="adsfpo" order="ASC" orderby="title"]

[/loop]

Any advice is appreciated.