I'm not sure if this will help you, but I extracted eDNA from Candida albicans biofilms and the protocol I applied can also be used for bacterial biofilms. However, I didn't evaluate eDNA in agarose gel.
This article includes the methodology of extraction of eDNA from bacterial biofilm and detection of eDNA by agarose gel electrophoresis. It applies to H. pylori, but it may be useful.
Thank you all for sharing important information. I will try to do the work as per the given protocol and if any queries are there I will get back to you.