Hi D.!
While using FCC in your file adapter you only have the option to skip some lines from the beginning of file, not at the end.
So, there are few ways you can go with your requirement.
First, create empty node for blank line and ignore it in further mapping.
Second, develop adapter module which will read your file and compose xml document from it where you could skip blank lines with java code.
Third (and the most preferrable), ask the source system programmers team to remove/not to create the last blank line during file creation procedure.
Regards, Evgeniy.