The difference would be that a temporary quota transfer would be for one season only. The permanent one would effectively be permanently moving some of that quota from one licence to another—so each year that it's reissued.
If I have 100 tonnes of something, for example, and somebody else has 100 tonnes, in certain fisheries the rules would permit me to transfer a portion of my quota, let's say 10 tonnes, to that other licence holder, either temporarily for this year only, or permanently, so that going forward, I would have 90 tonnes, and that other licence holder would have 110.