The 'Path Too long' problem might occur due to an earlier patch/upgrade that is applied.
While upgrading (applying PPM,) the files that are to be overwritten in the PPM will be backed up inside a folder named Patch.
The files inside this follow the same directory structure as the original and results in this error.
eg. ManageEngine/reports/webapps/ROOT/WEB-INF/web.xml will be moved to ManageEngine/reports/Patch/ZOHO_DB-3.1.00-SP-0.0.0/SERVER/ROOT.war/WEB-INF/web.xml
As the number of sub-folders increases, the path elongates and exceeds windows limit of 260 characters.
This will not affect the product in anyway, but will not let the files with lengthy path to be deleted or copied.
In this case, the you can ignore the un-copied files.