I believe FLT, Faster than Light Travel, is the more common of the two. Never actually seen FTL in that context.
I’ve only ever seen FTL, at least in science fiction (books, TV, etc.).
I also haven’t ever seen FLT anywhere; whenever people are discussing speeds in excess of c, it’s always FTL. What books are you reading, that use that apparently nonstandard abbreviation?
FLT stands for “faster-than-light travel” specifically, while FTL is used in other sentences involving “faster-than-light”, like FTL drive, or even FTL travel.
I’ve really never (until this thread, at least) seen FLT used instead of FTL travel. Usually, the context is clear enough that the “travel” part can be omitted anyway.