a <- "X/ZHEB100/TKN_VAR29380_timely_p1.txt"
a2 <- sub("^.*/([A-Z]{3})_VAR\\d+_timely(_[^_.]+)?\\.[^.]*$", "\\1\\2", a)
a2
b <- "X/ZHEB100/ZHN_VAR29380_timely.txt"
b2 <- sub("^.*/([A-Z]{3})_VAR\\d+_timely(_[^_.]+)?\\.[^.]*$", "\\1\\2", b)
b2