Just reset the levels of z$sigma (and also redefine sigmaExpr):
z$sigma <- factor(z$sigma,
levels = c(5,10,20,30,50)) # new levels order
sigmaExprList <- lapply(as.numeric(levels(z$sigma)),
function(s) bquote(sigma == .(s)))
sigmaExpr <- as.expression(sigmaExprList)
INUExpr <- paste0("INU = ", c(0,20,40), "%")
p <- bwplot(Error ~ Method | sigma + INU, data = z,
scales = list(rot=90), horiz = FALSE,
layout = c(5,3), col = "red")
useOuterStrips(p,
strip = strip.custom(
factor.levels = sigmaExpr),
strip.left = strip.custom(
factor.levels = INUExpr)
)