This isn't a Rule Machine thing; it's a general thing with the Import/Export/Clone utility. Victor is aware.
For now, re-creating the app is always an option (many of us remember when this was the only way ), or you can consider temporarily downgrading to a platform version from before the problem started (probably 2.4.4.146, though I don't see a mention of what platform version you're running, which is always helpful for reports).
In that case, you'd need the second option -- although, tangential to the point, I'd say using Rule 5.1 is now probably better unless you have a very specific need like direct access to a "legacy" global variable.