Most of our spaces use modified and styled left sidebar. With the demise of the Documentation theme, we restructured it to work with the default theme. There were a series of problems with this, the last one being discussed in CONF-41129. While we thought we were close to the end of these problems, the 2016-04-11 Cloud update broke us again as noted in the issue. This describes the automation we used to fix this.
Fortunately, we standardized all of our space specific side-bars consistently with a single page in each space called _LeftSide. The workaround was to change a specific span macro to a div. We also decided to change the id to avoid potential conflicts with future Confluence modifications from PageTree to PageTree_override.
--action runFromSpaceList --common "--action modifyPage --special \" # ~\" --comment \"span to div pagetree fix\" --space @space@ --title _LeftSide --findReplaceRegex \"<ac:structured-macro ac:macro-id=~[^~]*~ ac:name=~span~ ac:schema-version=~1~><ac:parameter ac:name=~id~>PageTree<#<ac:structured-macro ac:macro-id=~fab7f0fa-f05b-4f2a-9628-3c37989fdbab~ ac:name=~div~ ac:schema-version=~1~><ac:parameter ac:name=~id~>PageTree_override<\" "