Please note that my question pertains to custom folders.
There are 3 options when you Export using Discoverer Administrator, Entire EUL, Business Area, and Selected items. Use of Selected Items should only be done to move/backup Workbooks. If you were to select export Folder, only the Folder definition is exported. You would need to individually select every single item contained in the folder (fields, item classes, etc.) to get the content of the folder too. If done incorrectly, you will have orphaned folders (not associated with BA) and missing items.
So, though it is possible to export folders, it is very complicated and not recommended.
When importing you should import by Name and not identifier. The reason is every EUL can have a different identifier for the same item (BA, Folder, Field, etc.). Most Apps Mode (E-Business Suite database) EULs are created by Importing the Oracle EBS supplied content. So, EULA_US and EULB_US will have different identifiers. As long as the Names match it will work nicely. If the identifiers do not match, you will have two of everything that was imported.
One more note, when importing into a Apps Mode EUL, you should never, ever use the EUL owner (a database user).