At the moment it's not possible to add multiple folders to a TLT project if the original structure must be retained when creating target files. As a result, with large projects with hundreds of folders it's not possible to use TLT at all.
When using ZIP files with folder structure, the structure will be kept in the project roundtrip.
See here for more information:
(this is a blog about Trados Enterprise but the same capability applies to Trados Live Team)
and here
At the moment it's not possible to add multiple folders to a TLT project if the original structure must be retained when creating target files. As a result, with large projects with hundreds of folders it's not possible to use TLT at all.