It is unknown what happened to him after "Shredder & Splintered", but it was shown that Scrag was briefly turned back into a human, when Shredder was showing the Turtles and Splinter what will happen if a mutant is hit by his Retromutagen Ray Generator. But he is seen as a bat again later, behind bars in the Technodrome with the other mutants.
Additionally, he was seen as a human again in Turtles Forever, when both Turtles teams arrive on the 1987 Turtles' Earth. He is seen walking on the streets along Grunt.
As a noun, the word "scrag" means a person with a thin appearance. As a verb, it means to beat someone up. Both definitions fit Scrag as he is very skinny and is a punk.
His mutant form resembles Wingnut's Archie comics counterpart minus the wings.