b: times size db 0
a:
  file "a.bin"
  size = $ - a

source = a
destination = b
repeat size
  load x BYTE from source
  ; conversion goes here
  store BYTE x at destination
  source = source + 1
  destination = destination + 1
end repeat    

virtual
  file "a.bin"
  size = $
end virtual
  file "convert.bin": 0, size    

LOAD/STORE operate on target addresses, not the file offsets. So if your source contains multiple addressing
spaces, like the ones started with ORG directive, you have to make a "::" label for each one of them and then
use these labels to bytes from consecutive spaces. You may need to overload ORG with a macro and maintain
a symbolic list with labels of all the addressing spaces and their corresponding address ranges.

b: times size db 0

virtual at 0
a::
  file "a.bin"
  size = $
end virtual

destination = b
repeat size
  load x BYTE from a:(% - 1)
  ; conversion goes here
  store BYTE x at destination
  destination = destination + 1
end repeat
    

I had tried that, but it doesn't work on my beloved version 1.67.22 (with the listing facility) and I didn't
investigate it further.