I have a multi-project gradle build with 17 sub projects. When I started the multi-project build (and with small gradle projects) I was able to ditch the gradle idea plugin and just open the top level build.gradle within Idea. As a few more project have been added I find that every week or so Idea tries to rebuild the configuration from the build.gradle files. This can take hours to perform because it seems to get stuck somewhere. To stop this from happening I have had to revert back to the gradle plugin generating iml and ipr files rather than let Idea do it for me.
This could be related to git and switching branches, but whatever Idea is doing, I can completely rebuild the projects with a clean and build in a lot less time than Idea takes to rebuild the configuration.