Вы можете подгруппировать столбцы и строки и изменить значения на 0.
cols <- c('Oct', 'Nov', 'Dec', 'Jan')
x[x$Branch %in% y, cols] <- 0
x
# Oct Nov Dec Jan Branch Fin.Year Year State
#1 0 0 0 0 Chennai F.Y.2019-20 2020 TamilNadu
#2 0 0 0 0 Madurai F.Y.2020-21 2021 TamilNadu
#3 148 1 206 183 Coimbatore F.Y.2019-20 2020 TamilNadu
#4 0 1 180 140 Theni F.Y.2020-21 2021 TamilNadu
данные
x <- structure(list(Oct = c(143L, 0L, 148L, 0L), Nov = c(1L, 1L, 1L,
1L), Dec = c(89L, 101L, 206L, 180L), Jan = c(147L, 98L, 183L,
140L), Branch = c("Chennai", "Madurai", "Coimbatore", "Theni"
), Fin.Year = c("F.Y.2019-20", "F.Y.2020-21", "F.Y.2019-20",
"F.Y.2020-21"), Year = c(2020L, 2021L, 2020L, 2021L), State = c("TamilNadu",
"TamilNadu", "TamilNadu", "TamilNadu")), class = "data.frame",
row.names = c(NA, -4L))
y <- c("Chennai", "Madurai")