I used the new optimizer tool to run a report as part of my preparation for creating my new subdomain and turning on Lightning. I learned that one of my Conga Composer buttons has a hardcode URL for an associated report. After a quick chat with Conga support I learned: "Gathering data for Conga Composer using Salesforce reports will not work in the Lightning experience when My Domain is enabled. If you are using the Lightning experience, all reports will need to be replaced with queries to gather data for your Composer solutions."
For more information related to Conga and Lightning:
https://support.getconga.com/Notifications/Alert%3A_Enable_My_Domain_for_Spring_'17
For information on how to create Conga queries:
I ran across this as well. Creating Conga buttons that work in Lightning requires some manual updating. Hopefully Conga is planning to update their app to make Lightning button creation simpler.
I find that using the query editor in the Developer Console is a great way to test queries and to create more complex queries than the Conga query editor will support.
