I don't understand your problem, remove empty() function works as expected for me.
library(janitor)
df <- data.frame(col1 = c(NA, NA, NA, NA, NA),
col2 = c(NA, 2, 3, 4, 5)
)
df
#> col1 col2
#> 1 NA NA
#> 2 NA 2
#> 3 NA 3
#> 4 NA 4
#> 5 NA 5
remove_empty(df, which = c("rows"))
#> col1 col2
#> 2 NA 2
#> 3 NA 3
#> 4 NA 4
#> 5 NA 5
remove_empty(df, which = c("cols"))
#> col2
#> 1 NA
#> 2 2
#> 3 3
#> 4 4
#> 5 5
remove_empty(df)
#> value for "which" not specified, defaulting to c("rows", "cols")
#> col2
#> 2 2
#> 3 3
#> 4 4
#> 5 5
Created on 2019-01-16 by the reprex package (v0.2.1)