Not sure about disabling. Does happen all the time. I am under impression that it might for the first time when migrated the project. Once saved, it should be a 5.6 project. Isn't it the case?
This is where repository / SCM such as git / cvs / svn etc., would help even if something unexpected happens, one can always get it again from repository. And it helps every one in the team has the same copy of the project while starting the day and check-in the changes by EOD, so that no losing of work.
I don't think there is a nice solution to this problem. What you say makes sense in some cases, but not when the project was created in ReadyAPI for example like we have..also in other soapui versions.. Being about the creation moment, this would not be changed by loading the project in another tool.. will not override the data.
I figured it out that, in case we load the workspace with projects in the closed state, the warning messages will not be shown anymore. So this could be a workaround.