CertUtil -hashfile Output to File and Error Handling

I need to generate a file with hashfile tags from a list of files that is generated within the same batch file. Here is the code that I have so far:

@echo off
setlocal enabledelayedexpansion

:: Set the variables for this script.
set testfolder=c:\test\test folder
set listfile=c:\test\output\file list.txt
set hashfile=c:\test\output\hashes.txt

:: Delete any of the files that were created the last time this script was ran.
del "%hashfile%"
del "%listfile%"
cls

:: Generate a file with a list of all of the files (with path) in designated folder and subdirectories.
:: Directory and subdirectory names are not included in the list. Only files.
dir /s /b /a-d "%testfolder%" > "%listfile%"

:: Assign each line of the file above to its own variable.
set counter=1
for /f "usebackq delims=" %%x in ("%listfile%") do (
  set "line_!counter!=%%x"
  set /a counter+=1
)

:: Count the number of lines in the above file to use as a reference point.
set /a numlines=counter - 1

:: Generate an MD5 hash for each variable and write it to a file with a blank space between each.
for /l %%x in (1,1,%numlines%) do (
  certutil -hashfile "!line_%%x!" MD5 >> "%hashfile%"
  echo( >> "%hashfile%"
)
eof

For most of the files that I generate a hashfile for, I get something like:

MD5 hash of file c:\test\test folder\Citrix 2.bmp:
31 34 d6 04 cd b0 4b ef a7 63 c3 e9 ae a8 3d 01
CertUtil: -hashfile command completed successfully.

But there are times where I get an error like:

CertUtil: -hashfile command FAILED: 0x800703ee (WIN32: 1006)
CertUtil: The volume for a file has been externally altered so that the opened file is no longer valid.

1. Why would some files be giving this error?
2. How can I delete any line that begins with CertUtil: so I don't have unnecessary lines or is there a way to only write the first 2 lines of the CertUtil command to the file.
3. After the %hashfile% is in its final form, I want to run certutil -hashfile "%hashfile% MD5 and assign just the hash code to a variable. What is the syntax for that?

Slightly modified code snippet shows that 0x800703ee (WIN32: 1006 ERROR_FILE_INVALID) error message just for zero length files (cf. rem comments).

:: Generate an MD5 hash for each variable and write it to a file with a blank line...
>"%hashfile%" (
  for /l %%x in (1,1,%numlines%) do (

        rem debugging: show file length for each file
    for %%G in ("!line_%%x!") do echo(%%~zG "%%~G"

        rem operational: skip certutil for zero length files (requires elaboration)   
    certutil -hashfile "!line_%%x!" MD5
    echo(
  )
)

See Command Line arguments (Parameters) for %%~zG and "%%~G" explanation.