There's nothing particular to "chr" in the code that's giving you an error (copied below). compileCopyCountSegments() is pretty simply, and just a double loop over samples and over chromosomes.

Do you get an error with running copyCountSegments() alone on a single "fit" of class ExomeCopy?

copyCountSegments <- function(object) {
  x <- object@path
  changes <- which(x[-length(x)] != x[-1]) + 1
  if (length(changes) > 0) {
    range.start <- c(1,changes)
    range.end <- c(changes-1,length(x))
  } else {
    range.start <- 1
    range.end <- length(x)
  }
  targeted.bp <- sapply(1:length(range.start),function(i) sum(width(object@ranges)[[1]][range.start[i]:range.end[i]]))
  log.odds <- sapply(1:length(range.start),function(i) sum(object@log.odds[range.start[i]:range.end[i]]))
  gr <- GRanges(seqnames(object@ranges)[1],
                IRanges(start=start(object@ranges)[range.start],
                        end=end(object@ranges)[range.end]),
                copy.count=object@fx.par$S[as.numeric(x[range.start])],
                log.odds=round(log.odds,2),
                nranges=(range.end - range.start + 1),
                targeted.bp=targeted.bp,
                sample.name=object@sample.name)
  genome(gr) <- genome(object@ranges)
  gr
}

compileCopyCountSegments <- function(fit.list) {
  sample.res <- lapply(fit.list,function(seq.list) {
    seq.res <- lapply(seq.list, copyCountSegments)
    do.call(c,unname(seq.res))
  })
  do.call(c,unname(sample.res))
}