Seems to work?
Can you produce an example where it does not?
library(xcms)
library(faahKO)
cdfpath <- file.path(find.package("faahKO"), "cdf")
files <- list.files(cdfpath, recursive = TRUE)
xraw <- xcmsRaw(paste0(cdfpath,"/",files[1]))
xraw2 <- xcmsRaw(paste0(cdfpath,"/",files[2]))
plotEIC(xraw, add=FALSE)
plotEIC(xraw2, add=FALSE)
plotEIC(xraw, add=FALSE)
plotEIC(xraw2, add=TRUE,col="red")