File restore problems after systems loss

I need to restore files from a file backup. I need to copy files directly from the server as the target system has failed. When looking at the client folders I have a lot of incremental backups up until a date in time when the backups stopped working. When looking at the data on disk and the files in each folder they do not add up. Is there a way to build the incremental into a complete data set from day x to present day without using the webui as it never downloads the selection. The current folder is very miss leading as it is not a complete dataset to be copied from. I see a lot of people pointing to the administrative manual but its very limited. Maybe this is a feature thats needed?