I have a number of copies of a reference drawing clipped and rotated in another file to use for drawing interior elevations for multiple rooms. Each of the copies of the referenced drawing are clipped to only show the room that is being elevated above the referenced and clipped plan copies. The drawing will be working fine when last saved but randomly when the file is reopened all the clips will be lost, creating a rat's nest of over lapping plans. I then have to open an old version of the drawing where the clip are still intact and delete the old elevations and copy the updated drawing into the old version to restore the clipped reference drawings. Unloading and reloading the reference doesn't restore the clips, nor does running a rebuild or refresh... 

Well in the process of writing this post and trouble shooting to double check what wasn't working it turns out that all of the clips are being turned off for some reason randomly. If I select all of the references at once and run the 'clipreference' command and set them to 'on' the clips seem to be restored. Still not sure why they are being turned off in the first place.