I want to replicate my Fisheye production environment to my Fisheye lower Invironment. I have refreshed Database and now now I would like to know if i need to copy any folder manually from my production environment Fisheye home directory to lower environment home directory.
I don't really understand what you're trying to achieve but it's not recommend to mess with Fisheye&Crucible files.
The application store its data on a filesystem and database. That's why the only recommended way of creating backups is using built-in backup feature.
What I mean to say is that When we refresh our Confluence Lower Environment with Confluence production Environment we copy "attachment" folder from production environment to our lower environment manually so that the data on both the environment are same and synchronized.
Still not really sure what do you want to achieve.
Do you want to run test environment ? If so, I think you can create a backup and restore it to test environment, but make sure then you use different database, otherwise data in a production DB might be overwritten.