This has been an issue with Cloverleaf. I ask the release level so we can determine if it is still occurring in the latest release.
So essentially (as you have discovered) the GUI shows the changes but the changes are not posted to the actual file.
I have noted this happens most often inside IF Actions and ITERATES.
So what I have taken to doing in defense is to do part of my changes (inside and IF or ITERATE Action particularly), close the Xlate and open it to make sure the changes just made are there. It is not normally a reliably repeatable thus making diagnosing and fixing difficult and is certainly frustrating.
Fortunately it does not seem to happen with alarming frequency.
email: jim.kosloskey@jim-kosloskey.com 29+ years Cloverleaf, 59 years IT - old fart.