I faced the same problem with the last 3 updates.
Applying configuration changes after the update brings me to an unusable system. 502 Bad gateway error from the web interface. No more ssh access.
Rebooting and "undoing" the changes fixed it.
But actually no revert was done, the required update was still present. And working fine.
With the latest update (to version 6.0.43-1) I tried directly to select "undo changes" just after the update completion and this just closed the message. The system is updated. No more messages, no errors, no problemes.
Maybe some more experienced user has an explanation for this behaviour?
Seems to me... not very logical.