string <- "Junk1_Junk2_Junk3__ID1_Junk4_Junk5.pdf"
library(stringr)
stringr::str_extract(string, "[^_]+(?=(?:_[^_]*){2}$)")
## Base R:
sub(".*?([^_]+)(?:_[^_]*){2}$", "\\1", string)
c3RyaW5nIDwtICJKdW5rMV9KdW5rMl9KdW5rM19fSUQxX0p1bms0X0p1bms1LnBkZiIKbGlicmFyeShzdHJpbmdyKQpzdHJpbmdyOjpzdHJfZXh0cmFjdChzdHJpbmcsICJbXl9dKyg/PSg/Ol9bXl9dKil7Mn0kKSIpCgojIyBCYXNlIFI6CnN1YigiLio/KFteX10rKSg/Ol9bXl9dKil7Mn0kIiwgIlxcMSIsIHN0cmluZyk=