davout,
I could not replicate the issue at my end with MyEclipse 2014.
The steps I followed are :
1. Copied a java file from folder1 to folder2.
2. Right click on the java file in folder2 and click Rename.Give a different name and its renamed.
3. The java file in folder1 will still have the old name as the rename action is applicable only to the file in folder2.
Are you seeing any errors when trying to rename the file? Please give us exact steps and the exact error you are seeing.
Please check the .log file which is located at <workspace dir>/.,metdata/.log for any errors of interest. If any, paste them here for us to take a look.