The error message "Resource is out of sync" is displayed more often since Clover 4 when working on server project in designer.
Here is one of many examples when the "Resource is out of sync" error message is displayd in version 4 but not in version 3.5 of Clover:
1) create new plain text file anywhere in the sandbox;
2) make a copy of the plain text file created in previous step;
3) open copied version of the plain text file;
4) error message is displayed in case of version 4;