When you make any changes to a process, don't delete anything until you have your changes in. If you need to swap out any actions, statuses, etc, use the existing lines to connect the new ones and then delete anything you don't need any more once there are no connections to it.
We used to have this problem too, but we found that by doing this, we didn't get these errors any more.
Hope this helps.
I only deleted a few lines without deleting any other actions, status', etc and the process saved fine without any errors.
I will definitely keep this in mind on future edits. Thanks !!
Five years later and it still has this bug? What are they doing over there? Super annoying when you're trying to work out manually coding a calc for a precondition (that we shouldn't have to do in the first place) and oops...there goes all your work. Hope you saved it in notepad first!