Readxl Changing my Column Headers

I could reproduce the issue by making an xlsx file with decimal headers. You could use a regex to fix it up. The example below assumes that any time you have six zeroes (or nines, after looking at the linked issue) or more in a row after a number or decimal point, you want to discard everything from the zeroes/nines onward.

library(tibble)
library(stringr)
dat <-
  structure(
    list(
      `1.1000000000000001` = c("a", "b", "c"),
      `1.2` = c(1, 2, 3),
      `2.1` = c("d", "e", "f"),
      `2.2000000000000002` = c(4,                                                                                                                                   5, 6)
    ),
    .Names = c("1.1000000000000001", "1.2", "2.1", "2.2000000000000002"),
    class = c("tbl_df", "tbl", "data.frame"),
    row.names = c(NA,                                                                                                                                                                                                                                                                         -3L)
  )
dat
#> # A tibble: 3 x 4
#>   `1.1000000000000001` `1.2` `2.1` `2.2000000000000002`
#>                  <chr> <dbl> <chr>                <dbl>
#> 1                    a     1     d                    4
#> 2                    b     2     e                    5
#> 3                    c     3     f                    6
names(dat) <- names(dat) %>%
  str_replace("([.[:digit:]])[09]{6,}(\\d+?)", 
              "\\1")
dat
#> # A tibble: 3 x 4
#>   `1.1` `1.2` `2.1` `2.2`
#>   <chr> <dbl> <chr> <dbl>
#> 1     a     1     d     4
#> 2     b     2     e     5
#> 3     c     3     f     6